6-108686774-T-G

Position:

• chr6-108686774-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;