6-120777311-C-T

Variant names:

• chr6-120777311-C-T
• rs2817937

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 0.927 in 152,134 control chromosomes in the GnomAD database, including 65,357 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 0.93 (65357 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140879 AN: 152016 Hom.: 65308 Cov.: 31

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.927 AC: 140988 AN: 152134 Hom.: 65357 Cov.: 31 AF XY: 0.926 AC XY: 68866 AN XY: 74356

African (AFR) AF: 0.953 AC: 39559 AN: 41506

American (AMR) AF: 0.953 AC: 14565 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3282 AN: 3468

East Asian (EAS) AF: 0.982 AC: 5069 AN: 5162

South Asian (SAS) AF: 0.915 AC: 4409 AN: 4820

European-Finnish (FIN) AF: 0.878 AC: 9274 AN: 10564

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.907 AC: 61696 AN: 68006

Other (OTH) AF: 0.943 AC: 1994 AN: 2114

Alfa AF: 0.916 Hom.: 255181

Bravo AF: 0.935

Asia WGS AF: 0.942 AC: 3270 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.35
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2817937; hg19: chr6-121098457; COSMIC: COSV68194787;