6-116867572-C-T

Variant names:

• chr6-116867572-C-T
• rs339319

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 0.262 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.231

Alfa AF: 0.251 Hom.: 2866

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs339319; hg19: chr6-117188735;