rs7910154

Positions:

• chr10-30711464-A-G
• chr10-30711464-A-T

Variant summary

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

The ENST00000422642.6(SVIL2P):​n.2272A>G variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.775 in 540,722 control chromosomes in the GnomAD database, including 167,322 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 0.72 (41260 hom., cov: 30)
  • Exomes 𝑓: 0.80 (126062 hom.)
• Consequence: SVIL2P ENST00000422642.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.91

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=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SVIL2P	NR_036438.1	n.1471-1094A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SVIL2P	ENST00000422642.6	n.2272A>G		non_coding_transcript_exon_variant	16/19

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109341 AN: 151894 Hom.: 41261 Cov.: 30

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.747

GnomAD4 exome AF: 0.796 AC: 309488 AN: 388708 Hom.: 126062 Cov.: 0 AF XY: 0.804 AC XY: 174535 AN XY: 217110

Gnomad4 AFR exome AF: 0.465

Gnomad4 AMR exome AF: 0.646

Gnomad4 ASJ exome AF: 0.823

Gnomad4 EAS exome AF: 0.482

Gnomad4 SAS exome AF: 0.837

Gnomad4 FIN exome AF: 0.797

Gnomad4 NFE exome AF: 0.842

Gnomad4 OTH exome AF: 0.786

GnomAD4 genome AF: 0.719 AC: 109368 AN: 152014 Hom.: 41260 Cov.: 30 AF XY: 0.716 AC XY: 53221 AN XY: 74302

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.747

Alfa AF: 0.828 Hom.: 106004

Bravo AF: 0.698

Asia WGS AF: 0.690 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	14
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7910154; hg19: chr10-31000393;