rs12917114

Variant names:

• chr15-47852953-C-T
• rs12917114
• ENST00000662551.1:n.188+40037C>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+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
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662551.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259754	ENST00000662551.1		n.188+40037C>T		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.188+40037C>T		intron	N/A
	ENSG00000259754	ENST00000665188.1		n.68+40037C>T		intron	N/A

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

African (AFR) AF: 0.0479 AC: 1984 AN: 41456

American (AMR) AF: 0.134 AC: 2037 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0208 AC: 72 AN: 3468

East Asian (EAS) AF: 0.325 AC: 1673 AN: 5144

South Asian (SAS) AF: 0.129 AC: 618 AN: 4804

European-Finnish (FIN) AF: 0.148 AC: 1562 AN: 10526

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

European-Non Finnish (NFE) AF: 0.0870 AC: 5914 AN: 67956

Other (OTH) AF: 0.0859 AC: 181 AN: 2106

Alfa AF: 0.0844 Hom.: 313

Bravo AF: 0.0928

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.64
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12917114;

hg19: chr15-48145150;