rs353087

Variant names:

• chr3-15149080-T-C
• rs353087

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 0.539 in 152,038 control chromosomes in the GnomAD database, including 23,534 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 0.54 (23534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606

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 = 0.744 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: 0.539 AC: 81845 AN: 151920 Hom.: 23482 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.539 AC: 81962 AN: 152038 Hom.: 23534 Cov.: 32 AF XY: 0.544 AC XY: 40410 AN XY: 74298

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.532

Alfa AF: 0.430 Hom.: 7148

Bravo AF: 0.549

Asia WGS AF: 0.634 AC: 2204 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	2.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs353087; hg19: chr3-15190587;