6-127249415-C-T

Variant names:

• chr6-127249415-C-T
• rs6913350

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;