6-137922602-C-T

Variant names:

• chr6-137922602-C-T
• rs58721818

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0324 in 152,100 control chromosomes in the GnomAD database, including 88 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 0.032 (88 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0324 (4934/152100) while in subpopulation AFR AF = 0.0449 (1864/41484). AF 95% confidence interval is 0.0432. There are 88 homozygotes in GnomAd4. There are 2331 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 88 gene

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: 0.0325 AC: 4932 AN: 151982 Hom.: 88 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0404

Gnomad EAS AF: 0.0271

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.0167

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0264

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

GnomAD4 genome AF: 0.0324 AC: 4934 AN: 152100 Hom.: 88 Cov.: 32 AF XY: 0.0313 AC XY: 2331 AN XY: 74362

African (AFR) AF: 0.0449 AC: 1864 AN: 41484

American (AMR) AF: 0.0256 AC: 391 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0404 AC: 140 AN: 3468

East Asian (EAS) AF: 0.0272 AC: 141 AN: 5182

South Asian (SAS) AF: 0.0328 AC: 158 AN: 4824

European-Finnish (FIN) AF: 0.0167 AC: 177 AN: 10586

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0293 AC: 1995 AN: 67976

Other (OTH) AF: 0.0270 AC: 57 AN: 2108

Alfa AF: 0.0298 Hom.: 110

Bravo AF: 0.0325

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.81
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs58721818; hg19: chr6-138243739;