15-33259892-G-T

Variant names:

• chr15-33259892-G-T
• rs6495001
• ENST00000806662.1:n.439-13279C>A

Variant summary

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

The ENST00000806662.1(ENSG00000293377):​n.439-13279C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 151,854 control chromosomes in the GnomAD database, including 50,872 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 0.81 (50872 hom., cov: 30)
• Consequence: ENSG00000293377 ENST00000806662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• Publications: 1 publications found

Genes affected

ENSG00000293377 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806662.1. 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
	ENSG00000293377	ENST00000806662.1		n.439-13279C>A		intron	N/A
	ENSG00000293377	ENST00000806663.1		n.338-13279C>A		intron	N/A
	ENSG00000293377	ENST00000806664.1		n.119-13279C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122756 AN: 151738 Hom.: 50856 Cov.: 30

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.809 AC: 122820 AN: 151854 Hom.: 50872 Cov.: 30 AF XY: 0.818 AC XY: 60710 AN XY: 74194

African (AFR) AF: 0.607 AC: 25088 AN: 41328

American (AMR) AF: 0.884 AC: 13500 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3085 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5172

South Asian (SAS) AF: 0.943 AC: 4549 AN: 4824

European-Finnish (FIN) AF: 0.935 AC: 9837 AN: 10524

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58800 AN: 67954

Other (OTH) AF: 0.835 AC: 1762 AN: 2110

Alfa AF: 0.858 Hom.: 85098

Bravo AF: 0.796

Asia WGS AF: 0.942 AC: 3275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.97
DANN	Benign	0.51
PhyloP100		0.33

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: rs6495001;

hg19: chr15-33552093;