Genetic Variant ERMAP:p.Leu18Leu (chr1-42830502-C-T) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001017922.2(ERMAP):c.54C>T(p.Leu18Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 1,613,398 control chromosomes in the GnomAD database, including 47,097 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.20 ( 3663 hom., cov: 32)

Exomes 𝑓: 0.24 ( 43434 hom. )

Consequence

ERMAP
NM_001017922.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.73

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 1-42830502-C-T is Benign according to our data. Variant chr1-42830502-C-T is described in ClinVar as [Benign]. Clinvar id is 3058973.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERMAP	NM_001017922.2 link	c.54C>T	p.Leu18Leu	synonymous_variant	Exon 3 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.54C>T	p.Leu18Leu	synonymous_variant	Exon 3 of 12	1	NM_001017922.2	ENSP00000361595.2		Q96PL5

Frequencies

GnomAD3 genomes

AF:

0.204

AC:

31043

AN:

152006

Hom.:

3663

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.114

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.178

Gnomad EAS

AF:

0.0139

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.339

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.203

GnomAD3 exomes

AF:

0.224

AC:

56235

AN:

251416

Hom.:

7183

AF XY:

0.223

AC XY:

30249

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.111

Gnomad AMR exome

AF:

0.269

Gnomad ASJ exome

AF:

0.179

Gnomad EAS exome

AF:

0.0160

Gnomad SAS exome

AF:

0.176

Gnomad FIN exome

AF:

0.353

Gnomad NFE exome

AF:

0.251

Gnomad OTH exome

AF:

0.227

GnomAD4 exome

AF:

0.238

AC:

347185

AN:

1461274

Hom.:

43434

Cov.:

AF XY:

0.236

AC XY:

171801

AN XY:

726964

show subpopulations

Gnomad4 AFR exome

AF:

0.109

Gnomad4 AMR exome

AF:

0.266

Gnomad4 ASJ exome

AF:

0.178

Gnomad4 EAS exome

AF:

0.0172

Gnomad4 SAS exome

AF:

0.179

Gnomad4 FIN exome

AF:

0.350

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.215

GnomAD4 genome

AF:

0.204

AC:

31052

AN:

152124

Hom.:

3663

Cov.:

AF XY:

0.206

AC XY:

15343

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.111

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.178

Gnomad4 EAS

AF:

0.0139

Gnomad4 SAS

AF:

0.175

Gnomad4 FIN

AF:

0.339

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.201

Alfa

AF:

0.236

Hom.:

5775

Bravo

AF:

0.191

Asia WGS

AF:

0.0860

AC:

298

AN:

3478

EpiCase

AF:

0.241

EpiControl

AF:

0.244

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ERMAP-related disorder

Benign:1

Oct 21, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

0.52

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over