rs2414718

Variant names:

• chr15-61570934-G-A
• rs2414718
• ENST00000559783.2:n.123+18982C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-61570934-G-A
• chr15-61570934-G-C
• chr15-61570934-G-T

Variant summary

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

The ENST00000559783.2(ENSG00000259675):​n.123+18982C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,980 control chromosomes in the GnomAD database, including 21,652 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 0.53 (21652 hom., cov: 32)
• Consequence: ENSG00000259675 ENST00000559783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 12 publications found

Genes affected

ENSG00000259675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559783.2. 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
	ENSG00000259675	ENST00000559783.2	TSL:3	n.123+18982C>T		intron	N/A
	ENSG00000259675	ENST00000748013.1		n.346+18982C>T		intron	N/A
	ENSG00000297521	ENST00000748517.1		n.610-5316G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80034 AN: 151862 Hom.: 21648 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.527 AC: 80058 AN: 151980 Hom.: 21652 Cov.: 32 AF XY: 0.527 AC XY: 39139 AN XY: 74272

African (AFR) AF: 0.396 AC: 16420 AN: 41468

American (AMR) AF: 0.556 AC: 8477 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2102 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2750 AN: 5144

South Asian (SAS) AF: 0.580 AC: 2784 AN: 4802

European-Finnish (FIN) AF: 0.533 AC: 5632 AN: 10568

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40189 AN: 67956

Other (OTH) AF: 0.545 AC: 1151 AN: 2112

Alfa AF: 0.566 Hom.: 16927

Bravo AF: 0.516

Asia WGS AF: 0.541 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.69
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs2414718; hg19: chr15-61863133;