rs2460641

Variant names:

• chr15-45833571-A-C
• rs2460641
• ENST00000559600.1:n.96-15010A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-45833571-A-C
• chr15-45833571-A-G
• chr15-45833571-A-T

Variant summary

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

The ENST00000559600.1(ENSG00000259200):​n.96-15010A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,888 control chromosomes in the GnomAD database, including 10,911 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 0.37 (10911 hom., cov: 31)
• Consequence: ENSG00000259200 ENST00000559600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589
• Publications: 3 publications found

Genes affected

ENSG00000259200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559600.1. 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
	LOC105370802	NR_135680.1		n.96-15010A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259200	ENST00000559600.1	TSL:3	n.96-15010A>C		intron	N/A
	ENSG00000259200	ENST00000560705.1	TSL:3	n.557-15010A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56058 AN: 151770 Hom.: 10899 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.369 AC: 56112 AN: 151888 Hom.: 10911 Cov.: 31 AF XY: 0.373 AC XY: 27695 AN XY: 74228

African (AFR) AF: 0.466 AC: 19313 AN: 41436

American (AMR) AF: 0.447 AC: 6825 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1422 AN: 3464

East Asian (EAS) AF: 0.392 AC: 2015 AN: 5136

South Asian (SAS) AF: 0.411 AC: 1975 AN: 4802

European-Finnish (FIN) AF: 0.336 AC: 3540 AN: 10542

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19927 AN: 67938

Other (OTH) AF: 0.358 AC: 753 AN: 2106

Alfa AF: 0.318 Hom.: 26296

Bravo AF: 0.384

Asia WGS AF: 0.385 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.6
DANN	Benign	0.76
PhyloP100		0.59

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: rs2460641;

hg19: chr15-46125769;