rs1535043

Variant names:

• chr20-46139085-T-A
• rs1535043

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 0.364 in 152,100 control chromosomes in the GnomAD database, including 11,807 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 0.36 (11807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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: 0.364 AC: 55280 AN: 151982 Hom.: 11805 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.364 AC: 55297 AN: 152100 Hom.: 11807 Cov.: 32 AF XY: 0.366 AC XY: 27229 AN XY: 74322

African (AFR) AF: 0.139 AC: 5758 AN: 41508

American (AMR) AF: 0.428 AC: 6553 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1732 AN: 3472

East Asian (EAS) AF: 0.744 AC: 3841 AN: 5162

South Asian (SAS) AF: 0.469 AC: 2261 AN: 4820

European-Finnish (FIN) AF: 0.405 AC: 4289 AN: 10578

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29531 AN: 67952

Other (OTH) AF: 0.377 AC: 793 AN: 2106

Alfa AF: 0.394 Hom.: 1684

Bravo AF: 0.359

Asia WGS AF: 0.518 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1535043; hg19: chr20-44767724;