rs6138892

Variant names:

• chr20-2774842-T-C
• rs6138892

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 0.153 in 152,132 control chromosomes in the GnomAD database, including 1,881 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 0.15 (1881 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359

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 = 0.172 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: 0.153 AC: 23241 AN: 152014 Hom.: 1881 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.0948

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.153 AC: 23246 AN: 152132 Hom.: 1881 Cov.: 31 AF XY: 0.152 AC XY: 11334 AN XY: 74362

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.0947

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.133

Alfa AF: 0.168 Hom.: 3120

Bravo AF: 0.150

Asia WGS AF: 0.120 AC: 415 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	5.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6138892; hg19: chr20-2755488;