6-108686774-T-G

Variant names:

• chr6-108686774-T-G
• rs1268169

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 0.469 in 152,024 control chromosomes in the GnomAD database, including 18,952 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 0.47 (18952 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71146 AN: 151904 Hom.: 18917 Cov.: 32

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.469 AC: 71238 AN: 152024 Hom.: 18952 Cov.: 32 AF XY: 0.468 AC XY: 34790 AN XY: 74302

African (AFR) AF: 0.742 AC: 30749 AN: 41464

American (AMR) AF: 0.378 AC: 5782 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1104 AN: 3464

East Asian (EAS) AF: 0.304 AC: 1573 AN: 5166

South Asian (SAS) AF: 0.475 AC: 2284 AN: 4810

European-Finnish (FIN) AF: 0.412 AC: 4354 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23985 AN: 67970

Other (OTH) AF: 0.447 AC: 938 AN: 2100

Alfa AF: 0.332 Hom.: 1366

Bravo AF: 0.477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.095
DANN	Benign	0.56
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1268169; hg19: chr6-109007977; COSMIC: COSV59627102;