rs12917114

Variant names:

• chr15-47852953-C-T
• rs12917114
• ENST00000662551.1:n.188+40037C>T

Variant summary

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

The ENST00000662551.1(ENSG00000259754):​n.188+40037C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0936 in 151,906 control chromosomes in the GnomAD database, including 952 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 0.094 (952 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000662551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 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+40037C>T		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.188+40037C>T		intron_variant	Intron 1 of 5
ENSG00000259754	ENST00000665188.1	n.68+40037C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0937 AC: 14216 AN: 151786 Hom.: 954 Cov.: 31

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0936 AC: 14223 AN: 151906 Hom.: 952 Cov.: 31 AF XY: 0.0962 AC XY: 7139 AN XY: 74216

Gnomad4 AFR AF: 0.0479

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.0870

Gnomad4 OTH AF: 0.0859

Alfa AF: 0.0850 Hom.: 281

Bravo AF: 0.0928

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12917114; hg19: chr15-48145150;