rs10517023

chr4-23730595-C-Achr4-23730595-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507666.1(ERVH-1):n.91-2696G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374528	XR_925476.3	n.170-10853C>A		intron_variant, non_coding_transcript_variant
LOC105374528	XR_925477.3	n.169+11753C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ERVH-1	ENST00000507666.1	n.91-2696G>T		intron_variant, non_coding_transcript_variant		1
	ENST00000514290.1	n.118-37724C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.699

Alfa AF: 0.709 Hom.: 50420

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517023; hg19: chr4-23732218;