rs242544

chr20-32816341-A-G

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 0.674 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.862

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.615

Alfa AF: 0.620 Hom.: 6433

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs242544; hg19: chr20-31404147;