6-80961003-T-C

Variant names:

• chr6-80961003-T-C
• rs10485280

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 0.365 in 151,472 control chromosomes in the GnomAD database, including 10,174 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 0.36 (10174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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: 0.364 AC: 55147 AN: 151354 Hom.: 10146 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.365 AC: 55215 AN: 151472 Hom.: 10174 Cov.: 32 AF XY: 0.369 AC XY: 27332 AN XY: 74014

African (AFR) AF: 0.371 AC: 15345 AN: 41382

American (AMR) AF: 0.304 AC: 4613 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1128 AN: 3464

East Asian (EAS) AF: 0.557 AC: 2844 AN: 5108

South Asian (SAS) AF: 0.428 AC: 2061 AN: 4814

European-Finnish (FIN) AF: 0.404 AC: 4266 AN: 10558

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23812 AN: 67678

Other (OTH) AF: 0.358 AC: 751 AN: 2100

Alfa AF: 0.353 Hom.: 5406

Bravo AF: 0.356

Asia WGS AF: 0.455 AC: 1576 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.023
DANN	Benign	0.33
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10485280; hg19: chr6-81670720;