6-127249415-C-T

Variant names:

• chr6-127249415-C-T
• rs6913350

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 0.669 in 151,916 control chromosomes in the GnomAD database, including 34,432 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 0.67 (34432 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.71 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: 0.670 AC: 101647 AN: 151798 Hom.: 34428 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.669 AC: 101673 AN: 151916 Hom.: 34432 Cov.: 31 AF XY: 0.664 AC XY: 49243 AN XY: 74210

African (AFR) AF: 0.583 AC: 24159 AN: 41420

American (AMR) AF: 0.716 AC: 10926 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2394 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3399 AN: 5162

South Asian (SAS) AF: 0.535 AC: 2577 AN: 4816

European-Finnish (FIN) AF: 0.694 AC: 7316 AN: 10542

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48618 AN: 67938

Other (OTH) AF: 0.687 AC: 1447 AN: 2106

Alfa AF: 0.684 Hom.: 17567

Bravo AF: 0.671

Asia WGS AF: 0.567 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.10
DANN	Benign	0.77
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6913350; hg19: chr6-127570560;