rs742731

chr20-18905094-G-A

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 0.418 in 152,062 control chromosomes in the GnomAD database, including 13,552 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 0.42 (13552 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.418 AC: 63541 AN: 151944 Hom.: 13516 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.418 AC: 63633 AN: 152062 Hom.: 13552 Cov.: 33 AF XY: 0.417 AC XY: 30976 AN XY: 74330

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.424

Alfa AF: 0.402 Hom.: 10406

Bravo AF: 0.430

Asia WGS AF: 0.387 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.5
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs742731; hg19: chr20-18885738;