ENST00000754648.1:n.257G>A

Variant names:

• chr10-30676156-G-A
• rs11008171
• ENST00000754648.1:n.257G>A

Variant summary

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

The ENST00000754648.1(ENSG00000290952):​n.257G>A variant causes a non coding transcript exon 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: ENSG00000290952 ENST00000754648.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.43
• Publications: 3 publications found

Genes affected

ENSG00000290952 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000290952	ENST00000754648.1	n.257G>A		non_coding_transcript_exon_variant	Exon 2 of 5
SVIL2P	ENST00000422642.6	n.175+4477G>A		intron_variant	Intron 2 of 18	6
ENSG00000290952	ENST00000754647.1	n.235+554G>A		intron_variant	Intron 1 of 4
ENSG00000290952	ENST00000754649.1	n.224+554G>A		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.0951 AC: 3941 AN: 41454

American (AMR) AF: 0.161 AC: 2464 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3462

East Asian (EAS) AF: 0.118 AC: 608 AN: 5166

South Asian (SAS) AF: 0.154 AC: 744 AN: 4818

European-Finnish (FIN) AF: 0.190 AC: 1999 AN: 10542

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18166 AN: 67970

Other (OTH) AF: 0.222 AC: 467 AN: 2108

Alfa AF: 0.243 Hom.: 7952

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
PhyloP100		4.4

Splicing

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

Other links and lift over

dbSNP: rs11008171; hg19: chr10-30965085;