rs6132407

Variant names:

• chr20-2190984-C-T
• rs6132407

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 0.125 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.125 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

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.122

Alfa AF: 0.152 Hom.: 557

Bravo AF: 0.114

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6132407; hg19: chr20-2171630;