15-94889196-C-G

Variant names:

• chr15-94889196-C-G
• rs4562999
• ENST00000614581.1:n.17-12516C>G

Variant summary

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

The ENST00000618611.4(ENSG00000293024):​n.193+47945C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,898 control chromosomes in the GnomAD database, including 34,905 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 0.67 (34905 hom., cov: 30)
• Consequence: ENSG00000293024 ENST00000618611.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 0 publications found

Genes affected

ENSG00000293024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000618611.4. 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
	ENSG00000293024	ENST00000614581.1	TSL:5	n.17-12516C>G		intron	N/A
	ENSG00000293024	ENST00000615751.5	TSL:5	n.130+32333C>G		intron	N/A
	ENSG00000293024	ENST00000618377.1	TSL:5	n.330+32333C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101505 AN: 151780 Hom.: 34844 Cov.: 30

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.669 AC: 101623 AN: 151898 Hom.: 34905 Cov.: 30 AF XY: 0.669 AC XY: 49628 AN XY: 74214

African (AFR) AF: 0.813 AC: 33703 AN: 41432

American (AMR) AF: 0.593 AC: 9047 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3466

East Asian (EAS) AF: 0.879 AC: 4510 AN: 5130

South Asian (SAS) AF: 0.676 AC: 3256 AN: 4820

European-Finnish (FIN) AF: 0.580 AC: 6104 AN: 10530

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40930 AN: 67948

Other (OTH) AF: 0.629 AC: 1329 AN: 2112

Alfa AF: 0.619 Hom.: 3486

Bravo AF: 0.675

Asia WGS AF: 0.781 AC: 2716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.28
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4562999; hg19: chr15-95432425;