rs10995190

Variant names:

• chr10-62518923-G-A
• rs10995190
• ENST00000647733.1:c.981+59126G>A

Variant summary

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

The ENST00000647733.1(ENSG00000285837):​c.981+59126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,140 control chromosomes in the GnomAD database, including 1,887 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 0.15 (1887 hom., cov: 32)
• Consequence: ENSG00000285837 ENST00000647733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 139 publications found

Genes affected

ENSG00000285837 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 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
ENSG00000285837	ENST00000647733.1	c.981+59126G>A		intron_variant	Intron 4 of 7			ENSP00000502188.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23388 AN: 152022 Hom.: 1882 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.154 AC: 23404 AN: 152140 Hom.: 1887 Cov.: 32 AF XY: 0.155 AC XY: 11494 AN XY: 74386

African (AFR) AF: 0.174 AC: 7206 AN: 41512

American (AMR) AF: 0.115 AC: 1765 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3470

East Asian (EAS) AF: 0.0220 AC: 114 AN: 5186

South Asian (SAS) AF: 0.0855 AC: 413 AN: 4828

European-Finnish (FIN) AF: 0.222 AC: 2338 AN: 10550

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10568 AN: 67988

Other (OTH) AF: 0.151 AC: 320 AN: 2114

Alfa AF: 0.149 Hom.: 6713

Bravo AF: 0.147

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.8
DANN	Benign	0.65
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10995190; hg19: chr10-64278682; COSMIC: COSV67920557;