rs11210729

Positions:

• chr1-42840457-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ERMAP	NM_001017922.2	c.712+161G>A		intron_variant		ENST00000372517.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERMAP	ENST00000372517.8	c.712+161G>A		intron_variant		1	NM_001017922.2	P1
ZNF691-DT	ENST00000659750.1	n.521+2318C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.171

Alfa AF: 0.153 Hom.: 2618

Bravo AF: 0.169

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

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