chr1-42840457-G-A

Variant names:

• chr1-42840457-G-A
• rs11210729
• NM_001017922.2:c.712+161G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001017922.2(ERMAP):​c.712+161G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 151,884 control chromosomes in the GnomAD database, including 2,131 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2131 hom., cov: 32)
• Consequence: ERMAP NM_001017922.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 11 publications found

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]

ZNF691-DT (HGNC:55800): (ZNF691 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017922.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERMAP	NM_001017922.2	MANE Select	c.712+161G>A		intron	N/A	NP_001017922.1	Q96PL5
	ERMAP	NM_018538.4		c.712+161G>A		intron	N/A	NP_061008.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ERMAP	ENST00000372517.8	TSL:1 MANE Select	c.712+161G>A		intron	N/A	ENSP00000361595.2	Q96PL5
	ERMAP	ENST00000372514.7	TSL:1	c.712+161G>A		intron	N/A	ENSP00000361592.3	Q96PL5
	ERMAP	ENST00000328249.3	TSL:1	n.1480+161G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24217 AN: 151764 Hom.: 2126 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0962

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.174

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.160 AC: 24230 AN: 151884 Hom.: 2131 Cov.: 32 AF XY: 0.163 AC XY: 12074 AN XY: 74230

African (AFR) AF: 0.145 AC: 5986 AN: 41388

American (AMR) AF: 0.263 AC: 4008 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1215 AN: 5166

South Asian (SAS) AF: 0.180 AC: 866 AN: 4814

European-Finnish (FIN) AF: 0.132 AC: 1387 AN: 10542

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9578 AN: 67932

Other (OTH) AF: 0.171 AC: 361 AN: 2112

Alfa AF: 0.151 Hom.: 6208

Bravo AF: 0.169

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.61
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11210729; hg19: chr1-43306128; COSMIC: COSV60273800; COSMIC: COSV60273800;