rs10517023

Variant names:

• chr4-23730595-C-A
• rs10517023
• ENST00000507666.1:n.91-2696G>T

Your query was ambiguous. Multiple possible variants found:

• chr4-23730595-C-A
• chr4-23730595-C-G

Variant summary

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

The ENST00000507666.1(ERVH-1):​n.91-2696G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,008 control chromosomes in the GnomAD database, including 38,422 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 0.71 (38422 hom., cov: 32)
• Consequence: ERVH-1 ENST00000507666.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 1 publications found

Genes affected

ERVH-1 (HGNC:39053): (endogenous retrovirus group H member 1)

ENSG00000250137 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374528	XR_925476.3	n.170-10853C>A		intron_variant	Intron 1 of 3
LOC105374528	XR_925477.3	n.169+11753C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ERVH-1	ENST00000507666.1	n.91-2696G>T		intron_variant	Intron 1 of 3	1
ENSG00000250137	ENST00000514290.1	n.118-37724C>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107787 AN: 151890 Hom.: 38400 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.710 AC: 107862 AN: 152008 Hom.: 38422 Cov.: 32 AF XY: 0.708 AC XY: 52574 AN XY: 74290

African (AFR) AF: 0.714 AC: 29619 AN: 41472

American (AMR) AF: 0.767 AC: 11720 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2252 AN: 3464

East Asian (EAS) AF: 0.643 AC: 3314 AN: 5156

South Asian (SAS) AF: 0.534 AC: 2576 AN: 4820

European-Finnish (FIN) AF: 0.720 AC: 7607 AN: 10568

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48475 AN: 67936

Other (OTH) AF: 0.699 AC: 1475 AN: 2110

Alfa AF: 0.711 Hom.: 116108

Bravo AF: 0.718

Asia WGS AF: 0.577 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.041
DANN	Benign	0.69
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10517023; hg19: chr4-23732218;