rs6138150

Variant names:

• chr20-23866372-T-C
• rs6138150

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 0.178 in 151,922 control chromosomes in the GnomAD database, including 2,523 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 0.18 (2523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 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: 0.178 AC: 26972 AN: 151806 Hom.: 2525 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0925

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.178 AC: 26974 AN: 151922 Hom.: 2523 Cov.: 31 AF XY: 0.178 AC XY: 13187 AN XY: 74216

African (AFR) AF: 0.159 AC: 6571 AN: 41438

American (AMR) AF: 0.222 AC: 3385 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1631 AN: 5142

South Asian (SAS) AF: 0.141 AC: 679 AN: 4804

European-Finnish (FIN) AF: 0.150 AC: 1576 AN: 10538

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12248 AN: 67980

Other (OTH) AF: 0.174 AC: 366 AN: 2104

Alfa AF: 0.182 Hom.: 11402

Bravo AF: 0.186

Asia WGS AF: 0.191 AC: 666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.65
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6138150; hg19: chr20-23847009;