chr6-166960059-T-G

Variant names:

• chr6-166960059-T-G
• rs1819333

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 0.575 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.575 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

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.588

Alfa AF: 0.534 Hom.: 3978

Bravo AF: 0.590

Asia WGS AF: 0.665 AC: 2311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1819333; hg19: chr6-167373547;