6-170281387-G-T

Position:

• chr6-170281387-G-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 0.466 in 152,100 control chromosomes in the GnomAD database, including 17,688 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 0.47 (17688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70878 AN: 151982 Hom.: 17666 Cov.: 33

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.466 AC: 70939 AN: 152100 Hom.: 17688 Cov.: 33 AF XY: 0.472 AC XY: 35107 AN XY: 74364

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.485

Alfa AF: 0.456 Hom.: 7477

Bravo AF: 0.461

Asia WGS AF: 0.787 AC: 2734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.083
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1028488; hg19: chr6-170590475;