10-96797028-A-T

Position:

• chr10-96797028-A-T

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 0.367 in 152,010 control chromosomes in the GnomAD database, including 13,816 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 0.37 (13816 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -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 = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55739 AN: 151892 Hom.: 13775 Cov.: 31

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.367 AC: 55835 AN: 152010 Hom.: 13816 Cov.: 31 AF XY: 0.365 AC XY: 27129 AN XY: 74332

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.362

Alfa AF: 0.103 Hom.: 150

Bravo AF: 0.389

Asia WGS AF: 0.516 AC: 1794 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	2.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6584099; hg19: chr10-98556785;