6-67617137-C-T

Position:

• chr6-67617137-C-T

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 0.604 in 141,576 control chromosomes in the GnomAD database, including 25,368 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 0.60 (25368 hom., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 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: 0.604 AC: 85443 AN: 141474 Hom.: 25352 Cov.: 21

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.604 AC: 85499 AN: 141576 Hom.: 25368 Cov.: 21 AF XY: 0.610 AC XY: 41727 AN XY: 68388

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.619

Alfa AF: 0.590 Hom.: 3428

Bravo AF: 0.586

Asia WGS AF: 0.656 AC: 2277 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs875033; hg19: chr6-68327030;