rs11008171

Variant names:

• chr10-30676156-G-A
• rs11008171
• ENST00000422642.6:n.175+4477G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-30676156-G-A
• chr10-30676156-G-C
• chr10-30676156-G-T

Variant summary

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

The ENST00000422642.6(SVIL2P):​n.175+4477G>A variant causes a intron change. The variant allele was found at a frequency of 0.193 in 152,004 control chromosomes in the GnomAD database, including 3,317 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 0.19 (3317 hom., cov: 32)
• Consequence: SVIL2P ENST00000422642.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.43

Genes affected

SVIL2P (HGNC:44959): (supervillin family member 2, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SVIL2P	ENST00000422642.6	n.175+4477G>A		intron_variant	Intron 2 of 18	6

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29396 AN: 151886 Hom.: 3318 Cov.: 32

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.193 AC: 29394 AN: 152004 Hom.: 3317 Cov.: 32 AF XY: 0.188 AC XY: 13932 AN XY: 74288

Gnomad4 AFR AF: 0.0951

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.222

Alfa AF: 0.249 Hom.: 6425

Bravo AF: 0.189

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	19
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11008171; hg19: chr10-30965085;