rs10496176

Positions:

• chr2-69946497-T-C

Variant summary

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

The NR_170375.1(ASPRV1):​n.1101-13304A>G 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 0.2 in 152,176 control chromosomes in the GnomAD database, including 3,839 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 0.20 (3839 hom., cov: 32)
• Consequence: ASPRV1 NR_170375.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

ASPRV1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ASPRV1	NR_170375.1	n.1101-13304A>G		intron_variant, non_coding_transcript_variant
ASPRV1	NR_170376.1	n.701-2579A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30384 AN: 152058 Hom.: 3823 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.200 AC: 30436 AN: 152176 Hom.: 3839 Cov.: 32 AF XY: 0.207 AC XY: 15377 AN XY: 74412

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.233

Alfa AF: 0.176 Hom.: 6393

Bravo AF: 0.224

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496176; hg19: chr2-70173629; COSMIC: COSV52479749;