rs11008171

Positions:

• 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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SVIL2P	ENST00000422642.6	n.175+4477G>A		intron_variant, non_coding_transcript_variant

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;