6-120777311-C-T

Variant names:

• chr6-120777311-C-T
• rs2817937

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 0.927 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.927 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

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.953

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.943

Alfa AF: 0.916 Hom.: 136444

Bravo AF: 0.935

Asia WGS AF: 0.942 AC: 3270 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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