rs10806665

Variant names:

• chr6-169206998-C-A
• rs10806665

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 0.0764 in 152,030 control chromosomes in the GnomAD database, including 477 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 0.076 (477 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0915 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: 0.0764 AC: 11612 AN: 151912 Hom.: 479 Cov.: 33

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.0751

Gnomad SAS AF: 0.0540

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0764 AC: 11619 AN: 152030 Hom.: 477 Cov.: 33 AF XY: 0.0746 AC XY: 5540 AN XY: 74304

African (AFR) AF: 0.0940 AC: 3897 AN: 41474

American (AMR) AF: 0.0541 AC: 827 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3472

East Asian (EAS) AF: 0.0749 AC: 387 AN: 5166

South Asian (SAS) AF: 0.0542 AC: 261 AN: 4812

European-Finnish (FIN) AF: 0.0645 AC: 680 AN: 10546

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0772 AC: 5244 AN: 67966

Other (OTH) AF: 0.0711 AC: 150 AN: 2110

Alfa AF: 0.0791 Hom.: 221

Bravo AF: 0.0765

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.51
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs10806665; hg19: chr6-169607093;