6-129751411-T-C

Variant names:

• chr6-129751411-T-C
• rs208865

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 0.936 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.896 AC: 37126 AN: 41448

American (AMR) AF: 0.952 AC: 14553 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3319 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5175 AN: 5178

South Asian (SAS) AF: 0.961 AC: 4629 AN: 4818

European-Finnish (FIN) AF: 0.937 AC: 9912 AN: 10582

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64534 AN: 68014

Other (OTH) AF: 0.922 AC: 1948 AN: 2112

Alfa AF: 0.941 Hom.: 101300

Bravo AF: 0.935

Asia WGS AF: 0.977 AC: 3397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs208865; hg19: chr6-130072556;