rs1386166

Positions:

• chr15-53297283-G-A

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 0.396 in 152,054 control chromosomes in the GnomAD database, including 12,467 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 0.40 (12467 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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 (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60296 AN: 151936 Hom.: 12477 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.396 AC: 60276 AN: 152054 Hom.: 12467 Cov.: 33 AF XY: 0.400 AC XY: 29747 AN XY: 74332

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.417

Alfa AF: 0.435 Hom.: 9482

Bravo AF: 0.386

Asia WGS AF: 0.372 AC: 1297 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	0.98
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1386166; hg19: chr15-53589480;