rs6042018

Variant names:

• chr20-1403654-T-C
• rs6042018

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 0.41 in 151,926 control chromosomes in the GnomAD database, including 13,460 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 0.41 (13460 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.410 AC: 62171 AN: 151808 Hom.: 13439 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.410 AC: 62244 AN: 151926 Hom.: 13460 Cov.: 31 AF XY: 0.410 AC XY: 30485 AN XY: 74268

African (AFR) AF: 0.464 AC: 19221 AN: 41404

American (AMR) AF: 0.522 AC: 7962 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3470

East Asian (EAS) AF: 0.695 AC: 3576 AN: 5148

South Asian (SAS) AF: 0.502 AC: 2414 AN: 4812

European-Finnish (FIN) AF: 0.220 AC: 2328 AN: 10576

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23777 AN: 67942

Other (OTH) AF: 0.448 AC: 945 AN: 2110

Alfa AF: 0.379 Hom.: 46376

Bravo AF: 0.439

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.65
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs6042018; hg19: chr20-1384298;