rs12915366

Variant names:

• chr15-78539411-G-A
• rs12915366
• ENST00000746668.1:n.131-136C>T

Variant summary

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

The ENST00000746668.1(ENSG00000297264):​n.131-136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,118 control chromosomes in the GnomAD database, including 8,456 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 0.31 (8456 hom., cov: 33)
• Consequence: ENSG00000297264 ENST00000746668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16
• Publications: 22 publications found

Genes affected

ENSG00000297264 (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 (NFE) allele frequency at 95% confidence interval = 0.413 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
ENSG00000297264	ENST00000746668.1	n.131-136C>T		intron_variant	Intron 1 of 2
ENSG00000297264	ENST00000746669.1	n.107+805C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47617 AN: 152000 Hom.: 8459 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.313 AC: 47626 AN: 152118 Hom.: 8456 Cov.: 33 AF XY: 0.310 AC XY: 23090 AN XY: 74364

African (AFR) AF: 0.162 AC: 6713 AN: 41516

American (AMR) AF: 0.249 AC: 3806 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3468

East Asian (EAS) AF: 0.165 AC: 852 AN: 5176

South Asian (SAS) AF: 0.341 AC: 1647 AN: 4826

European-Finnish (FIN) AF: 0.371 AC: 3923 AN: 10560

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28336 AN: 67958

Other (OTH) AF: 0.316 AC: 667 AN: 2112

Alfa AF: 0.379 Hom.: 19500

Bravo AF: 0.297

Asia WGS AF: 0.271 AC: 942 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	5.3
DANN	Benign	0.45
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs12915366; hg19: chr15-78831753;