rs242544

Variant names:

• chr20-32816341-A-G
• rs242544

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 0.674 in 152,008 control chromosomes in the GnomAD database, including 36,150 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 0.67 (36150 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.673 AC: 102258 AN: 151890 Hom.: 36088 Cov.: 31

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.674 AC: 102379 AN: 152008 Hom.: 36150 Cov.: 31 AF XY: 0.675 AC XY: 50116 AN XY: 74296

African (AFR) AF: 0.862 AC: 35737 AN: 41466

American (AMR) AF: 0.659 AC: 10062 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2094 AN: 3464

East Asian (EAS) AF: 0.995 AC: 5130 AN: 5154

South Asian (SAS) AF: 0.747 AC: 3598 AN: 4814

European-Finnish (FIN) AF: 0.539 AC: 5689 AN: 10562

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38036 AN: 67954

Other (OTH) AF: 0.615 AC: 1298 AN: 2110

Alfa AF: 0.627 Hom.: 6748

Bravo AF: 0.691

Asia WGS AF: 0.866 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.48
DANN	Benign	0.37
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs242544; hg19: chr20-31404147;