6-116867572-C-T

Variant names:

• chr6-116867572-C-T
• rs339319

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 0.262 in 152,048 control chromosomes in the GnomAD database, including 5,438 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 0.26 (5438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.417 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: 0.262 AC: 39802 AN: 151928 Hom.: 5432 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.262 AC: 39841 AN: 152048 Hom.: 5438 Cov.: 32 AF XY: 0.267 AC XY: 19835 AN XY: 74316

African (AFR) AF: 0.226 AC: 9388 AN: 41480

American (AMR) AF: 0.252 AC: 3860 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3468

East Asian (EAS) AF: 0.432 AC: 2231 AN: 5164

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4818

European-Finnish (FIN) AF: 0.306 AC: 3235 AN: 10570

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18314 AN: 67940

Other (OTH) AF: 0.231 AC: 487 AN: 2112

Alfa AF: 0.255 Hom.: 4248

Bravo AF: 0.254

Asia WGS AF: 0.396 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.1
DANN	Benign	0.36
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs339319; hg19: chr6-117188735;