6-108686319-A-G

Variant names:

• chr6-108686319-A-G
• rs1268170

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 0.47 in 152,084 control chromosomes in the GnomAD database, including 19,051 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 (19051 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 5 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 = 0.738 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: 0.469 AC: 71320 AN: 151964 Hom.: 19016 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.470 AC: 71412 AN: 152084 Hom.: 19051 Cov.: 32 AF XY: 0.469 AC XY: 34875 AN XY: 74328

African (AFR) AF: 0.745 AC: 30876 AN: 41472

American (AMR) AF: 0.380 AC: 5804 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1572 AN: 5166

South Asian (SAS) AF: 0.475 AC: 2288 AN: 4818

European-Finnish (FIN) AF: 0.413 AC: 4354 AN: 10554

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

European-Non Finnish (NFE) AF: 0.353 AC: 23996 AN: 68000

Other (OTH) AF: 0.447 AC: 946 AN: 2114

Alfa AF: 0.388 Hom.: 33739

Bravo AF: 0.477

Asia WGS AF: 0.454 AC: 1581 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	1.3
DANN	Benign	0.51
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1268170; hg19: chr6-109007522; COSMIC: COSV59627099;