dbSNP rs56025238: ERMAP:p.Gly57Arg (chr1-42830851-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001017922.2(ERMAP):c.169G>A(p.Gly57Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00271 in 1,607,760 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 8 hom. )

Consequence

ERMAP
NM_001017922.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter P:1B:1

Conservation

PhyloP100: 0.434

Publications

17 publications found

Variant links:

Genes affected

ERMAP (HGNC:15743): (erythroblast membrane associated protein (Scianna blood group)) The protein encoded by this gene is a cell surface transmembrane protein that may act as an erythroid cell receptor, possibly as a mediator of cell adhesion. Polymorphisms in this gene are responsible for the Scianna/Radin blood group system. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ERMAP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.04339391).

BP6

Variant 1-42830851-G-A is Benign according to our data. Variant chr1-42830851-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1916.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 8 BG gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERMAP	NM_001017922.2 link	c.169G>A	p.Gly57Arg	missense_variant	Exon 4 of 12	ENST00000372517.8	NP_001017922.1	Q96PL5A0A1C9HIH9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERMAP	ENST00000372517.8 link	c.169G>A	p.Gly57Arg	missense_variant	Exon 4 of 12	1	NM_001017922.2	ENSP00000361595.2		Q96PL5

Frequencies

GnomAD3 genomes

AF:

0.00184

AC:

280

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00404

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00309

Gnomad OTH

AF:

0.00143

GnomAD2 exomes

AF:

0.00189

AC:

451

AN:

238326

AF XY:

0.00200

show subpopulations

Gnomad AFR exome

AF:

0.000334

Gnomad AMR exome

AF:

0.000935

Gnomad ASJ exome

AF:

0.00296

Gnomad EAS exome

AF:

0.000172

Gnomad FIN exome

AF:

0.000147

Gnomad NFE exome

AF:

0.00307

Gnomad OTH exome

AF:

0.00204

GnomAD4 exome

AF:

0.00280

AC:

4073

AN:

1455454

Hom.:

Cov.:

AF XY:

0.00280

AC XY:

2026

AN XY:

723540

show subpopulations

African (AFR)

AF:

0.000240

AC:

AN:

33290

American (AMR)

AF:

0.00101

AC:

AN:

43522

Ashkenazi Jewish (ASJ)

AF:

0.00262

AC:

AN:

26000

East Asian (EAS)

AF:

0.000280

AC:

AN:

39324

South Asian (SAS)

AF:

0.000938

AC:

AN:

85292

European-Finnish (FIN)

AF:

0.000264

AC:

AN:

52964

Middle Eastern (MID)

AF:

0.00260

AC:

AN:

5762

European-Non Finnish (NFE)

AF:

0.00333

AC:

3696

AN:

1109166

Other (OTH)

AF:

0.00228

AC:

137

AN:

60134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

255

510

766

1021

1276

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

134

268

402

536

670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00184

AC:

280

AN:

152306

Hom.:

Cov.:

AF XY:

0.00187

AC XY:

139

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.000409

AC:

AN:

41568

American (AMR)

AF:

0.00170

AC:

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00404

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00124

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.000377

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00309

AC:

210

AN:

68014

Other (OTH)

AF:

0.00142

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00270

Hom.:

Bravo

AF:

0.00177

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00285

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00302

AC:

ExAC

AF:

0.00181

AC:

220

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Pathogenic:1Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SCIANNA BLOOD GROUP SYSTEM, SC:-1,2

Pathogenic:1

Jan 15, 2003

OMIM

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:literature only

- -

not specified

Benign:1

Jan 01, 2019

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.51

CADD

Benign

(source)

DANN

Benign

0.74

DEOGEN2

Benign

0.0024

T;T

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.78

FATHMM_MKL

Benign

0.047

LIST_S2

Benign

0.63

.;T

M_CAP

Benign

0.0085

MetaRNN

Benign

0.043

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.94

L;L

PhyloP100

0.43

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.63

N;N

REVEL

Benign

0.040

Sift

Benign

0.15

T;T

Sift4G

Benign

0.21

T;T

Polyphen

0.51

P;P

Vest4

0.23

MutPred

0.55

Gain of MoRF binding (P = 0.0072);Gain of MoRF binding (P = 0.0072);

MVP

0.32

MPC

0.21

ClinPred

0.0064

GERP RS

1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.12

gMVP

0.45

Mutation Taster

=97/3

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over