rs12324326

Variant names:

• chr15-47855938-C-T
• rs12324326
• ENST00000662551.1:n.188+43022C>T

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+43022C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,016 control chromosomes in the GnomAD database, including 1,378 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 0.12 (1378 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 0 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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
ENSG00000259754	ENST00000662551.1	n.188+43022C>T		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.188+43022C>T		intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1	n.68+43022C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18491 AN: 151898 Hom.: 1378 Cov.: 32

Gnomad AFR AF: 0.0910

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.122 AC: 18505 AN: 152016 Hom.: 1378 Cov.: 32 AF XY: 0.126 AC XY: 9323 AN XY: 74282

African (AFR) AF: 0.0911 AC: 3777 AN: 41462

American (AMR) AF: 0.173 AC: 2643 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0242 AC: 84 AN: 3468

East Asian (EAS) AF: 0.338 AC: 1747 AN: 5166

South Asian (SAS) AF: 0.139 AC: 666 AN: 4804

European-Finnish (FIN) AF: 0.177 AC: 1866 AN: 10546

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7297 AN: 67984

Other (OTH) AF: 0.114 AC: 241 AN: 2108

Alfa AF: 0.103 Hom.: 1112

Bravo AF: 0.120

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.19
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12324326; hg19: chr15-48148135;