6-108686774-T-G

Variant names:

• chr6-108686774-T-G
• rs1268169

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.468 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

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.447

Alfa AF: 0.314 Hom.: 1148

Bravo AF: 0.477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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