10-63129151-T-C

Variant names:

• chr10-63129151-T-C
• rs10995450

Variant summary

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

The variant allele was found at a frequency of 0.652 in 152,022 control chromosomes in the GnomAD database, including 35,414 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 0.65 (35414 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.81 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

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99165 AN: 151904 Hom.: 35437 Cov.: 30

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.652 AC: 99129 AN: 152022 Hom.: 35414 Cov.: 30 AF XY: 0.652 AC XY: 48436 AN XY: 74300

African (AFR) AF: 0.389 AC: 16136 AN: 41440

American (AMR) AF: 0.531 AC: 8097 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2894 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2005 AN: 5162

South Asian (SAS) AF: 0.706 AC: 3399 AN: 4812

European-Finnish (FIN) AF: 0.836 AC: 8834 AN: 10572

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55482 AN: 68000

Other (OTH) AF: 0.644 AC: 1357 AN: 2106

Alfa AF: 0.572 Hom.: 10098

Bravo AF: 0.613

Asia WGS AF: 0.500 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.1
DANN	Benign	0.80
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs10995450; hg19: chr10-64888911;