ENST00000422642.6:n.2272A>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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=-0.55).
• 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 rank	MANE	Protein	UniProt
SVIL2P	NR_036438.1	n.1471-1094A>G		intron_variant	Intron 8 of 9

Ensembl

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

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

African (AFR) AF: 0.465 AC: 4790 AN: 10308

American (AMR) AF: 0.646 AC: 18371 AN: 28430

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 11035 AN: 13404

East Asian (EAS) AF: 0.482 AC: 7318 AN: 15196

South Asian (SAS) AF: 0.837 AC: 49636 AN: 59282

European-Finnish (FIN) AF: 0.797 AC: 21693 AN: 27228

Middle Eastern (MID) AF: 0.852 AC: 1870 AN: 2196

European-Non Finnish (NFE) AF: 0.842 AC: 179127 AN: 212758

Other (OTH) AF: 0.786 AC: 15648 AN: 19906

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

African (AFR) AF: 0.492 AC: 20365 AN: 41426

American (AMR) AF: 0.675 AC: 10311 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2825 AN: 3472

East Asian (EAS) AF: 0.532 AC: 2740 AN: 5146

South Asian (SAS) AF: 0.827 AC: 3970 AN: 4800

European-Finnish (FIN) AF: 0.805 AC: 8512 AN: 10570

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58019 AN: 68006

Other (OTH) AF: 0.747 AC: 1572 AN: 2104

Alfa AF: 0.806 Hom.: 159764

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
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;