6-170281387-G-T

Variant names:

• chr6-170281387-G-T
• rs1028488

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 0.466 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.342 AC: 14181 AN: 41484

American (AMR) AF: 0.492 AC: 7518 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3470

East Asian (EAS) AF: 0.992 AC: 5133 AN: 5176

South Asian (SAS) AF: 0.596 AC: 2875 AN: 4820

European-Finnish (FIN) AF: 0.528 AC: 5583 AN: 10574

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32391 AN: 67978

Other (OTH) AF: 0.485 AC: 1022 AN: 2106

Alfa AF: 0.464 Hom.: 10533

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1028488; hg19: chr6-170590475;