rs12441404

Variant names:

• chr15-92473682-G-A
• rs12441404
• ENST00000556865.1:n.760+572G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556865.1(C15orf32):​n.760+572G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,064 control chromosomes in the GnomAD database, including 10,777 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 0.37 (10777 hom., cov: 33)
• Consequence: C15orf32 ENST00000556865.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 2 publications found

Genes affected

C15orf32 (HGNC:26549): (chromosome 15 putative open reading frame 32)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C15orf32	NR_161370.1	n.966+610G>A		intron_variant	Intron 2 of 2
C15orf32	NR_161371.1	n.1004+572G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C15orf32	ENST00000556865.1	n.760+572G>A		intron_variant	Intron 2 of 2	1
C15orf32	ENST00000624458.1	n.989+610G>A		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56173 AN: 151946 Hom.: 10771 Cov.: 33

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.370 AC: 56199 AN: 152064 Hom.: 10777 Cov.: 33 AF XY: 0.377 AC XY: 28045 AN XY: 74330

African (AFR) AF: 0.450 AC: 18646 AN: 41464

American (AMR) AF: 0.426 AC: 6518 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1074 AN: 3472

East Asian (EAS) AF: 0.470 AC: 2431 AN: 5174

South Asian (SAS) AF: 0.396 AC: 1907 AN: 4816

European-Finnish (FIN) AF: 0.378 AC: 3994 AN: 10576

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20484 AN: 67964

Other (OTH) AF: 0.368 AC: 775 AN: 2108

Alfa AF: 0.352 Hom.: 1618

Bravo AF: 0.374

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.28
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12441404; hg19: chr15-93016912;