rs12912184

Variant names:

• chr15-92314871-G-A
• rs12912184
• ENST00000561674.1:n.41-1686C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561674.1(ENSG00000260661):​n.41-1686C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,100 control chromosomes in the GnomAD database, including 2,344 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 0.16 (2344 hom., cov: 32)
• Consequence: ENSG00000260661 ENST00000561674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

ENSG00000260661 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 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
ENSG00000260661	ENST00000561674.1	n.41-1686C>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24157 AN: 151982 Hom.: 2325 Cov.: 32

Gnomad AFR AF: 0.0674

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.159 AC: 24195 AN: 152100 Hom.: 2344 Cov.: 32 AF XY: 0.168 AC XY: 12517 AN XY: 74356

Gnomad4 AFR AF: 0.0673

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.164

Alfa AF: 0.169 Hom.: 4664

Bravo AF: 0.141

Asia WGS AF: 0.301 AC: 1043 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	9.1
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12912184; hg19: chr15-92858101;