15-36457229-A-C

Variant names:

• chr15-36457229-A-C
• rs2444728
• ENST00000558262.5:n.122+3099T>G

Variant summary

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

The ENST00000558262.5(ENSG00000259737):​n.122+3099T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,070 control chromosomes in the GnomAD database, including 65,440 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 0.92 (65440 hom., cov: 31)
• Consequence: ENSG00000259737 ENST00000558262.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 1 publications found

Genes affected

ENSG00000259737 (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 (NFE) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370768	XR_932110.1	n.248+6016A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259737	ENST00000558262.5	n.122+3099T>G		intron_variant	Intron 1 of 2	5
ENSG00000259737	ENST00000558875.1	n.205+11650T>G		intron_variant	Intron 2 of 3	3
ENSG00000296959	ENST00000743889.1	n.376+6016A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140566 AN: 151952 Hom.: 65400 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.925 AC: 140661 AN: 152070 Hom.: 65440 Cov.: 31 AF XY: 0.924 AC XY: 68709 AN XY: 74346

African (AFR) AF: 0.817 AC: 33846 AN: 41426

American (AMR) AF: 0.937 AC: 14316 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3333 AN: 3472

East Asian (EAS) AF: 0.864 AC: 4465 AN: 5168

South Asian (SAS) AF: 0.911 AC: 4389 AN: 4818

European-Finnish (FIN) AF: 0.978 AC: 10352 AN: 10580

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66782 AN: 68014

Other (OTH) AF: 0.945 AC: 1994 AN: 2110

Alfa AF: 0.963 Hom.: 96665

Bravo AF: 0.914

Asia WGS AF: 0.903 AC: 3141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.8
DANN	Benign	0.67
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs2444728; hg19: chr15-36749430;