rs2412524

Variant names:

• chr15-40501062-G-T
• rs2412524
• ENST00000561460.5:n.168-7270G>T

Variant summary

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

The ENST00000776324.1(ENSG00000259536):​n.170-7270G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,066 control chromosomes in the GnomAD database, including 5,873 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 0.25 (5873 hom., cov: 32)
• Consequence: ENSG00000259536 ENST00000776324.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 10 publications found

Genes affected

ENSG00000259536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776324.1. 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
	ENSG00000259536	ENST00000561460.5	TSL:5	n.168-7270G>T		intron	N/A
	ENSG00000259536	ENST00000776324.1		n.170-7270G>T		intron	N/A
	ENSG00000259536	ENST00000776325.1		n.169-7270G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38193 AN: 151948 Hom.: 5870 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.0860

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.251 AC: 38196 AN: 152066 Hom.: 5873 Cov.: 32 AF XY: 0.256 AC XY: 19031 AN XY: 74300

African (AFR) AF: 0.0782 AC: 3248 AN: 41522

American (AMR) AF: 0.245 AC: 3739 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.0864 AC: 448 AN: 5184

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4818

European-Finnish (FIN) AF: 0.416 AC: 4379 AN: 10538

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22803 AN: 67974

Other (OTH) AF: 0.263 AC: 554 AN: 2110

Alfa AF: 0.296 Hom.: 1289

Bravo AF: 0.227

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.69
PhyloP100		-0.023

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: rs2412524;

hg19: chr15-40793261;