Genetic Variant NM_001017922.2:c.-2G>A (chr1-42830447-G-A) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_001017922.2(ERMAP):c.-2G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 1,612,754 control chromosomes in the GnomAD database, including 43,690 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.27 ( 6389 hom., cov: 31)

Exomes 𝑓: 0.22 ( 37301 hom. )

Consequence

ERMAP
NM_001017922.2 5_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.54

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 made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 1-42830447-G-A is Benign according to our data. Variant chr1-42830447-G-A is described in ClinVar as [Benign]. Clinvar id is 3060601.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr1-42830447-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ERMAP	NM_001017922.2 link	c.-2G>A		5_prime_UTR_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 link	c.-2G>A		5_prime_UTR_variant	Exon 3 of 12	1	NM_001017922.2	ENSP00000361595.2		Q96PL5

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40354

AN:

151810

Hom.:

6376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.430

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.404

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.194

Gnomad OTH

AF:

0.237

GnomAD3 exomes

AF:

0.235

AC:

58963

AN:

251426

Hom.:

8330

AF XY:

0.241

AC XY:

32713

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.430

Gnomad AMR exome

AF:

0.135

Gnomad ASJ exome

AF:

0.225

Gnomad EAS exome

AF:

0.403

Gnomad SAS exome

AF:

0.375

Gnomad FIN exome

AF:

0.128

Gnomad NFE exome

AF:

0.194

Gnomad OTH exome

AF:

0.212

GnomAD4 exome

AF:

0.216

AC:

314937

AN:

1460826

Hom.:

37301

Cov.:

AF XY:

0.220

AC XY:

159903

AN XY:

726818

show subpopulations

Gnomad4 AFR exome

AF:

0.434

Gnomad4 AMR exome

AF:

0.138

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.352

Gnomad4 SAS exome

AF:

0.373

Gnomad4 FIN exome

AF:

0.130

Gnomad4 NFE exome

AF:

0.198

Gnomad4 OTH exome

AF:

0.235

GnomAD4 genome

AF:

0.266

AC:

40404

AN:

151928

Hom.:

6389

Cov.:

AF XY:

0.265

AC XY:

19670

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.430

Gnomad4 AMR

AF:

0.179

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.404

Gnomad4 SAS

AF:

0.358

Gnomad4 FIN

AF:

0.130

Gnomad4 NFE

AF:

0.194

Gnomad4 OTH

AF:

0.242

Alfa

AF:

0.222

Hom.:

3174

Bravo

AF:

0.275

Asia WGS

AF:

0.408

AC:

1421

AN:

3478

EpiCase

AF:

0.198

EpiControl

AF:

0.201

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

-0.87

CADD

Benign

7.9

DANN

Benign

0.85

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.26

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.26

Position offset: 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