rs1358087

Variant names:

• chr3-126360047-C-T
• rs1358087

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 0.632 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.658 AC: 27270 AN: 41450

American (AMR) AF: 0.588 AC: 8995 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2492 AN: 5164

South Asian (SAS) AF: 0.595 AC: 2861 AN: 4808

European-Finnish (FIN) AF: 0.617 AC: 6517 AN: 10566

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43659 AN: 67964

Other (OTH) AF: 0.630 AC: 1325 AN: 2104

Alfa AF: 0.633 Hom.: 88940

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1358087; hg19: chr3-126078890;