rs1429759

Variant names:

• chr3-137937756-C-A
• rs1429759

Your query was ambiguous. Multiple possible variants found:

• chr3-137937756-C-A
• chr3-137937756-C-G
• chr3-137937756-C-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 0.523 in 151,952 control chromosomes in the GnomAD database, including 23,246 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 0.52 (23246 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 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: 0.523 AC: 79453 AN: 151832 Hom.: 23240 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.523 AC: 79478 AN: 151952 Hom.: 23246 Cov.: 31 AF XY: 0.527 AC XY: 39111 AN XY: 74254

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.570

Alfa AF: 0.462 Hom.: 1546

Bravo AF: 0.503

Asia WGS AF: 0.642 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1429759; hg19: chr3-137656598;