10-96797028-A-T

Variant names:

• chr10-96797028-A-T
• rs6584099

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 0.367 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.698 AC: 28927 AN: 41438

American (AMR) AF: 0.298 AC: 4546 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1106 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2473 AN: 5174

South Asian (SAS) AF: 0.417 AC: 2011 AN: 4820

European-Finnish (FIN) AF: 0.177 AC: 1871 AN: 10592

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.204 AC: 13870 AN: 67958

Other (OTH) AF: 0.362 AC: 762 AN: 2106

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
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs6584099; hg19: chr10-98556785;