ENST00000422642.6:n.2272A>T

Variant names:

• chr10-30711464-A-T
• rs7910154
• ENST00000422642.6:n.2272A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000422642.6(SVIL2P):​n.2272A>T variant causes a non coding transcript exon change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SVIL2P ENST00000422642.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.91
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SVIL2P	NR_036438.1	n.1471-1094A>T		intron_variant	Intron 8 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SVIL2P	ENST00000422642.6	n.2272A>T		non_coding_transcript_exon_variant	Exon 16 of 19	6

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 389894 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 217742

African (AFR) AF: 0.00 AC: 0 AN: 10368

American (AMR) AF: 0.00 AC: 0 AN: 28514

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13440

East Asian (EAS) AF: 0.00 AC: 0 AN: 15334

South Asian (SAS) AF: 0.00 AC: 0 AN: 59342

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27346

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2202

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 213360

Other (OTH) AF: 0.00 AC: 0 AN: 19988

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		7.9

Splicing

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

Other links and lift over

dbSNP: rs7910154; hg19: chr10-31000393;