rs10081169

Variant names:

• chr6-46777651-T-G
• rs10081169

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 0.12 in 151,968 control chromosomes in the GnomAD database, including 2,815 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 0.12 (2815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.120 AC: 18236 AN: 151850 Hom.: 2801 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.0861

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.120 AC: 18286 AN: 151968 Hom.: 2815 Cov.: 32 AF XY: 0.119 AC XY: 8807 AN XY: 74294

African (AFR) AF: 0.358 AC: 14791 AN: 41340

American (AMR) AF: 0.0632 AC: 966 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0603 AC: 209 AN: 3464

East Asian (EAS) AF: 0.0128 AC: 66 AN: 5172

South Asian (SAS) AF: 0.0855 AC: 412 AN: 4818

European-Finnish (FIN) AF: 0.0129 AC: 137 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0213 AC: 1447 AN: 67972

Other (OTH) AF: 0.104 AC: 220 AN: 2110

Alfa AF: 0.0749 Hom.: 432

Bravo AF: 0.138

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.35
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10081169; hg19: chr6-46745388;