rs1545026

Variant names:

• chr3-194859643-C-A
• rs1545026

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 0.113 in 152,138 control chromosomes in the GnomAD database, including 1,056 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 0.11 (1056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.83
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 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: 0.113 AC: 17135 AN: 152020 Hom.: 1056 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.113 AC: 17137 AN: 152138 Hom.: 1056 Cov.: 32 AF XY: 0.108 AC XY: 8058 AN XY: 74370

African (AFR) AF: 0.105 AC: 4353 AN: 41504

American (AMR) AF: 0.0968 AC: 1479 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5182

South Asian (SAS) AF: 0.0955 AC: 460 AN: 4816

European-Finnish (FIN) AF: 0.0815 AC: 862 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9212 AN: 67986

Other (OTH) AF: 0.121 AC: 255 AN: 2108

Alfa AF: 0.127 Hom.: 1390

Bravo AF: 0.113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.054
DANN	Benign	0.55
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1545026; hg19: chr3-194580372;