chr6-166960059-T-G

Variant names:

• chr6-166960059-T-G
• rs1819333

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 0.575 in 152,130 control chromosomes in the GnomAD database, including 26,170 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 0.58 (26170 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• Publications: 76 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87386 AN: 152012 Hom.: 26122 Cov.: 33

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.575 AC: 87492 AN: 152130 Hom.: 26170 Cov.: 33 AF XY: 0.581 AC XY: 43176 AN XY: 74366

African (AFR) AF: 0.732 AC: 30386 AN: 41498

American (AMR) AF: 0.612 AC: 9358 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1830 AN: 3468

East Asian (EAS) AF: 0.621 AC: 3208 AN: 5170

South Asian (SAS) AF: 0.696 AC: 3357 AN: 4826

European-Finnish (FIN) AF: 0.534 AC: 5646 AN: 10574

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31798 AN: 67992

Other (OTH) AF: 0.588 AC: 1237 AN: 2104

Alfa AF: 0.593 Hom.: 11725

Bravo AF: 0.590

Asia WGS AF: 0.665 AC: 2311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.43
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1819333; hg19: chr6-167373547;