rs1542535

chr3-137347020-A-Gchr3-137347020-A-T

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 0.726 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.773

Alfa AF: 0.848 Hom.: 107553

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1542535; hg19: chr3-137065862;