rs6132407

Variant names:

• chr20-2190984-C-T
• rs6132407

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 0.125 in 152,200 control chromosomes in the GnomAD database, including 1,566 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 (1566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19059 AN: 152082 Hom.: 1569 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.125 AC: 19042 AN: 152200 Hom.: 1566 Cov.: 32 AF XY: 0.126 AC XY: 9382 AN XY: 74424

African (AFR) AF: 0.0291 AC: 1210 AN: 41544

American (AMR) AF: 0.114 AC: 1741 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3468

East Asian (EAS) AF: 0.144 AC: 749 AN: 5186

South Asian (SAS) AF: 0.143 AC: 688 AN: 4816

European-Finnish (FIN) AF: 0.194 AC: 2059 AN: 10596

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11536 AN: 67986

Other (OTH) AF: 0.122 AC: 257 AN: 2114

Alfa AF: 0.124 Hom.: 595

Bravo AF: 0.114

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs6132407; hg19: chr20-2171630;