rs4749580

Variant names:

• chr10-30685245-T-C
• rs4749580
• ENST00000422642.6:n.176-17T>C

Variant summary

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

The ENST00000422642.6(SVIL2P):​n.176-17T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 1,612,386 control chromosomes in the GnomAD database, including 136,838 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 0.36 (10574 hom., cov: 33)
  • Exomes 𝑓: 0.41 (126264 hom.)
• Consequence: SVIL2P ENST00000422642.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 7 publications found

Genes affected

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

ENSG00000290952 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 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.176-17T>C		intron_variant	Intron 2 of 18	6
ENSG00000290952	ENST00000754647.1	n.236-17T>C		intron_variant	Intron 1 of 4
ENSG00000290952	ENST00000754648.1	n.307-17T>C		intron_variant	Intron 2 of 4
ENSG00000290952	ENST00000754649.1	n.225-17T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54965 AN: 152064 Hom.: 10567 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.372

GnomAD4 exome AF: 0.412 AC: 602260 AN: 1460204 Hom.: 126264 Cov.: 36 AF XY: 0.415 AC XY: 301157 AN XY: 726430

African (AFR) AF: 0.239 AC: 7981 AN: 33446

American (AMR) AF: 0.460 AC: 20552 AN: 44676

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 9906 AN: 26098

East Asian (EAS) AF: 0.226 AC: 8967 AN: 39694

South Asian (SAS) AF: 0.471 AC: 40602 AN: 86186

European-Finnish (FIN) AF: 0.362 AC: 19340 AN: 53368

Middle Eastern (MID) AF: 0.368 AC: 2112 AN: 5740

European-Non Finnish (NFE) AF: 0.423 AC: 469286 AN: 1110656

Other (OTH) AF: 0.390 AC: 23514 AN: 60340

GnomAD4 genome AF: 0.361 AC: 54993 AN: 152182 Hom.: 10574 Cov.: 33 AF XY: 0.359 AC XY: 26740 AN XY: 74398

African (AFR) AF: 0.247 AC: 10267 AN: 41530

American (AMR) AF: 0.410 AC: 6273 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1314 AN: 5182

South Asian (SAS) AF: 0.467 AC: 2252 AN: 4820

European-Finnish (FIN) AF: 0.356 AC: 3771 AN: 10590

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28755 AN: 67988

Other (OTH) AF: 0.368 AC: 776 AN: 2110

Alfa AF: 0.393 Hom.: 1500

Bravo AF: 0.359

Asia WGS AF: 0.329 AC: 1145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.40
DANN	Benign	0.70
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4749580; hg19: chr10-30974174;