rs963336

Variant names:

• chr10-12882440-A-G
• rs963336
• ENST00000649832.1:n.510+4236A>G

Variant summary

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

The ENST00000649832.1(ENSG00000285520):​n.510+4236A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 152,012 control chromosomes in the GnomAD database, including 22,973 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 0.55 (22973 hom., cov: 31)
• Consequence: ENSG00000285520 ENST00000649832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

Genes affected

ENSG00000285520 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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
ENSG00000285520	ENST00000649832.1	n.510+4236A>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82895 AN: 151892 Hom.: 22961 Cov.: 31

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.546 AC: 82949 AN: 152012 Hom.: 22973 Cov.: 31 AF XY: 0.543 AC XY: 40376 AN XY: 74300

Gnomad4 AFR AF: 0.619 AC: 0.619275 AN: 0.619275

Gnomad4 AMR AF: 0.438 AC: 0.437934 AN: 0.437934

Gnomad4 ASJ AF: 0.601 AC: 0.601153 AN: 0.601153

Gnomad4 EAS AF: 0.496 AC: 0.495736 AN: 0.495736

Gnomad4 SAS AF: 0.544 AC: 0.544057 AN: 0.544057

Gnomad4 FIN AF: 0.532 AC: 0.531581 AN: 0.531581

Gnomad4 NFE AF: 0.529 AC: 0.529015 AN: 0.529015

Gnomad4 OTH AF: 0.536 AC: 0.536493 AN: 0.536493

Alfa AF: 0.522 Hom.: 3568

Bravo AF: 0.541

Asia WGS AF: 0.576 AC: 2006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs963336; hg19: chr10-12924440;