rs963335

Variant names:

• chr10-12882659-C-G
• rs963335
• ENST00000649832.1:n.510+4455C>G

Your query was ambiguous. Multiple possible variants found:

• chr10-12882659-C-G
• chr10-12882659-C-T

Variant summary

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

The ENST00000649832.1(ENSG00000285520):​n.510+4455C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,140 control chromosomes in the GnomAD database, including 3,176 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 0.13 (3176 hom., cov: 32)
• Consequence: ENSG00000285520 ENST00000649832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

ENSG00000285520 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 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+4455C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19264 AN: 152022 Hom.: 3164 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0225

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.127 AC: 19323 AN: 152140 Hom.: 3176 Cov.: 32 AF XY: 0.123 AC XY: 9181 AN XY: 74378

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.0622

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0225

Gnomad4 OTH AF: 0.117

Alfa AF: 0.00754 Hom.: 6

Bravo AF: 0.140

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs963335; hg19: chr10-12924659;