chr10-62501439-A-C

Position:

• chr10-62501439-A-C

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 0.178 in 152,050 control chromosomes in the GnomAD database, including 3,205 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 0.18 (3205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.178 AC: 26979 AN: 151932 Hom.: 3194 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.178 AC: 27023 AN: 152050 Hom.: 3205 Cov.: 32 AF XY: 0.178 AC XY: 13264 AN XY: 74318

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.0986

Gnomad4 OTH AF: 0.162

Alfa AF: 0.113 Hom.: 1928

Bravo AF: 0.184

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16917302; hg19: chr10-64261198;