15-94592952-C-T

Variant names:

• chr15-94592952-C-T
• rs4476132
• ENST00000784859.1:n.205-7810C>T

Variant summary

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

The ENST00000784859.1(ENSG00000259331):​n.205-7810C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,092 control chromosomes in the GnomAD database, including 45,297 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 0.77 (45297 hom., cov: 32)
• Consequence: ENSG00000259331 ENST00000784859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 3 publications found

Genes affected

ENSG00000259331 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784859.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259331	ENST00000784859.1		n.205-7810C>T		intron	N/A
	ENSG00000259331	ENST00000784860.1		n.49+3595C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116389 AN: 151974 Hom.: 45265 Cov.: 32

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.766 AC: 116479 AN: 152092 Hom.: 45297 Cov.: 32 AF XY: 0.766 AC XY: 56967 AN XY: 74322

African (AFR) AF: 0.906 AC: 37634 AN: 41536

American (AMR) AF: 0.816 AC: 12472 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2291 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3774 AN: 5166

South Asian (SAS) AF: 0.815 AC: 3922 AN: 4812

European-Finnish (FIN) AF: 0.693 AC: 7315 AN: 10556

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46486 AN: 67966

Other (OTH) AF: 0.773 AC: 1623 AN: 2100

Alfa AF: 0.712 Hom.: 19899

Bravo AF: 0.782

Asia WGS AF: 0.782 AC: 2716 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.9
DANN	Benign	0.33
PhyloP100		-0.089

Splicing

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

Other links and lift over

dbSNP: rs4476132; hg19: chr15-95136181;