rs4749580

chr10-30685245-T-C

Variant summary

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

The ENST00000422642.6(SVIL2P):n.176-17T>C variant causes a splice polypyrimidine tract, intron, non coding transcript 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 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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=-0.83).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SVIL2P	ENST00000422642.6	n.176-17T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.239

Gnomad4 AMR exome AF: 0.460

Gnomad4 ASJ exome AF: 0.380

Gnomad4 EAS exome AF: 0.226

Gnomad4 SAS exome AF: 0.471

Gnomad4 FIN exome AF: 0.362

Gnomad4 NFE exome AF: 0.423

Gnomad4 OTH exome AF: 0.390

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

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.368

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4749580; hg19: chr10-30974174;