rs2413914

Variant names:

• chr15-48812311-C-T
• rs2413914
• ENST00000826415.1:n.97-1464C>T

Variant summary

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

The ENST00000826415.1(ENSG00000259700):​n.97-1464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 152,174 control chromosomes in the GnomAD database, including 53,190 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 0.83 (53190 hom., cov: 32)
• Consequence: ENSG00000259700 ENST00000826415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 1 publications found

Genes affected

ENSG00000259700 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826415.1. 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
	ENSG00000259700	ENST00000826415.1		n.97-1464C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126409 AN: 152058 Hom.: 53142 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.831 AC: 126513 AN: 152174 Hom.: 53190 Cov.: 32 AF XY: 0.836 AC XY: 62202 AN XY: 74396

African (AFR) AF: 0.697 AC: 28927 AN: 41482

American (AMR) AF: 0.900 AC: 13773 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3165 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5185 AN: 5188

South Asian (SAS) AF: 0.925 AC: 4458 AN: 4818

European-Finnish (FIN) AF: 0.864 AC: 9143 AN: 10586

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58955 AN: 68018

Other (OTH) AF: 0.852 AC: 1798 AN: 2110

Alfa AF: 0.861 Hom.: 28901

Bravo AF: 0.828

Asia WGS AF: 0.948 AC: 3298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.13
DANN	Benign	0.88
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2413914; hg19: chr15-49104508;