rs1386166

Variant names:

• chr15-53297283-G-A
• rs1386166

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 0.396 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.282 AC: 11680 AN: 41486

American (AMR) AF: 0.431 AC: 6582 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3470

East Asian (EAS) AF: 0.436 AC: 2255 AN: 5174

South Asian (SAS) AF: 0.426 AC: 2055 AN: 4820

European-Finnish (FIN) AF: 0.440 AC: 4647 AN: 10560

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30067 AN: 67954

Other (OTH) AF: 0.417 AC: 880 AN: 2112

Alfa AF: 0.436 Hom.: 15122

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
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs1386166; hg19: chr15-53589480;