rs1542535

Variant names:

• chr3-137347020-A-G
• rs1542535

Your query was ambiguous. Multiple possible variants found:

• chr3-137347020-A-G
• chr3-137347020-A-T

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 0.726 in 152,060 control chromosomes in the GnomAD database, including 42,786 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 0.73 (42786 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.854 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: 0.726 AC: 110370 AN: 151942 Hom.: 42762 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.726 AC: 110423 AN: 152060 Hom.: 42786 Cov.: 31 AF XY: 0.727 AC XY: 54016 AN XY: 74336

African (AFR) AF: 0.431 AC: 17863 AN: 41456

American (AMR) AF: 0.856 AC: 13073 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.888 AC: 3082 AN: 3470

East Asian (EAS) AF: 0.661 AC: 3406 AN: 5156

South Asian (SAS) AF: 0.826 AC: 3981 AN: 4818

European-Finnish (FIN) AF: 0.745 AC: 7880 AN: 10576

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58464 AN: 67992

Other (OTH) AF: 0.773 AC: 1632 AN: 2112

Alfa AF: 0.824 Hom.: 220675

Bravo AF: 0.718

Asia WGS AF: 0.744 AC: 2586 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.27
DANN	Benign	0.80
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1542535; hg19: chr3-137065862;