10-63129151-T-C

Variant names:

• chr10-63129151-T-C
• rs10995450

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.644

Alfa AF: 0.624 Hom.: 3565

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10995450; hg19: chr10-64888911;