15-99959160-A-G

Variant names:

• chr15-99959160-A-G
• rs745104
• ENST00000528696.4:n.55-2155A>G

Variant summary

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

The ENST00000528696.4(ENSG00000259363):​n.55-2155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,114 control chromosomes in the GnomAD database, including 44,026 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 0.76 (44026 hom., cov: 32)
• Consequence: ENSG00000259363 ENST00000528696.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 12 publications found

Genes affected

ENSG00000259363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528696.4. 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
	ENSG00000259363	ENST00000528696.4	TSL:2	n.55-2155A>G		intron	N/A
	ENSG00000259363	ENST00000717141.1		n.866-2155A>G		intron	N/A
	ENSG00000259363	ENST00000743923.1		n.368-2155A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115379 AN: 151996 Hom.: 43997 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.759 AC: 115451 AN: 152114 Hom.: 44026 Cov.: 32 AF XY: 0.757 AC XY: 56270 AN XY: 74360

African (AFR) AF: 0.789 AC: 32739 AN: 41474

American (AMR) AF: 0.696 AC: 10642 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2438 AN: 3472

East Asian (EAS) AF: 0.588 AC: 3043 AN: 5176

South Asian (SAS) AF: 0.701 AC: 3379 AN: 4822

European-Finnish (FIN) AF: 0.786 AC: 8310 AN: 10576

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52359 AN: 67996

Other (OTH) AF: 0.722 AC: 1522 AN: 2108

Alfa AF: 0.756 Hom.: 178853

Bravo AF: 0.749

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
DANN	Benign	0.44
PhyloP100		0.23

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: rs745104;

hg19: chr15-100499365;