rs1358087

Variant names:

• chr3-126360047-C-T
• rs1358087

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 0.632 in 152,018 control chromosomes in the GnomAD database, including 30,488 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 0.63 (30488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 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: 0.632 AC: 96034 AN: 151902 Hom.: 30463 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.632 AC: 96102 AN: 152018 Hom.: 30488 Cov.: 32 AF XY: 0.630 AC XY: 46832 AN XY: 74316

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.630

Alfa AF: 0.634 Hom.: 50698

Bravo AF: 0.626

Asia WGS AF: 0.534 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358087; hg19: chr3-126078890;