6-127249415-C-T

Position:

• chr6-127249415-C-T

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 0.669 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.687

Alfa AF: 0.682 Hom.: 15505

Bravo AF: 0.671

Asia WGS AF: 0.567 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6913350; hg19: chr6-127570560;