6-166172137-C-G

Variant names:

• chr6-166172137-C-G
• rs1001979

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 0.13 in 152,172 control chromosomes in the GnomAD database, including 1,701 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 0.13 (1701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 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: 0.130 AC: 19699 AN: 152054 Hom.: 1704 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.0924

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.130 AC: 19712 AN: 152172 Hom.: 1701 Cov.: 32 AF XY: 0.133 AC XY: 9897 AN XY: 74374

African (AFR) AF: 0.205 AC: 8506 AN: 41494

American (AMR) AF: 0.0819 AC: 1253 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2071 AN: 5180

South Asian (SAS) AF: 0.0931 AC: 449 AN: 4822

European-Finnish (FIN) AF: 0.143 AC: 1515 AN: 10586

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0772 AC: 5252 AN: 68016

Other (OTH) AF: 0.122 AC: 256 AN: 2104

Alfa AF: 0.0349 Hom.: 32

Bravo AF: 0.132

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.29
DANN	Benign	0.81
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1001979; hg19: chr6-166585625;