6-129751411-T-C

Variant names:

• chr6-129751411-T-C
• rs208865

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 0.936 in 152,108 control chromosomes in the GnomAD database, including 66,710 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 0.94 (66710 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.936 AC: 142236 AN: 151992 Hom.: 66656 Cov.: 31

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.936 AC: 142348 AN: 152108 Hom.: 66710 Cov.: 31 AF XY: 0.935 AC XY: 69541 AN XY: 74364

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.952

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.922

Alfa AF: 0.942 Hom.: 80137

Bravo AF: 0.935

Asia WGS AF: 0.977 AC: 3397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208865; hg19: chr6-130072556;