15-78622903-C-T

Variant names:

• chr15-78622903-C-T
• rs6495309
• ENST00000821537.1:n.210+2593C>T

Variant summary

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

The ENST00000821537.1(ENSG00000259555):​n.210+2593C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 150,948 control chromosomes in the GnomAD database, including 6,026 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 0.27 (6026 hom., cov: 30)
• Consequence: ENSG00000259555 ENST00000821537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 91 publications found

Genes affected

ENSG00000259555 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821537.1. 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
	ENSG00000259555	ENST00000821537.1		n.210+2593C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40192 AN: 150854 Hom.: 6007 Cov.: 30

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.330

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.267 AC: 40240 AN: 150948 Hom.: 6026 Cov.: 30 AF XY: 0.274 AC XY: 20153 AN XY: 73630

African (AFR) AF: 0.251 AC: 10295 AN: 41070

American (AMR) AF: 0.434 AC: 6585 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2372 AN: 5150

South Asian (SAS) AF: 0.434 AC: 2070 AN: 4774

European-Finnish (FIN) AF: 0.272 AC: 2767 AN: 10174

Middle Eastern (MID) AF: 0.328 AC: 95 AN: 290

European-Non Finnish (NFE) AF: 0.215 AC: 14595 AN: 67830

Other (OTH) AF: 0.280 AC: 586 AN: 2096

Alfa AF: 0.234 Hom.: 4846

Bravo AF: 0.280

Asia WGS AF: 0.475 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.2
DANN	Benign	0.78
PhyloP100		-0.69

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: rs6495309;

hg19: chr15-78915245;