6-67617137-C-T

Variant names:

• chr6-67617137-C-T
• rs875033

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;