chr6-170584930-G-T

Position:

• chr6-170584930-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 0.472 in 152,070 control chromosomes in the GnomAD database, including 17,690 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 (17690 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.763 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: 0.472 AC: 71718 AN: 151952 Hom.: 17651 Cov.: 33

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.472 AC: 71801 AN: 152070 Hom.: 17690 Cov.: 33 AF XY: 0.473 AC XY: 35136 AN XY: 74334

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.453

Alfa AF: 0.366 Hom.: 1481

Bravo AF: 0.481

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs734249; hg19: chr6-170894018;