chr15-36882201-C-A

Variant names:

• chr15-36882201-C-A
• rs12910772
• ENST00000558089.1:n.316+129G>T

Variant summary

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

The ENST00000558089.1(ENSG00000259280):​n.316+129G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,108 control chromosomes in the GnomAD database, including 1,857 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 0.15 (1856 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: ENSG00000259280 ENST00000558089.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.800
• Publications: 4 publications found

Genes affected

ENSG00000259280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC145845	NR_024264.1	n.316+129G>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259280	ENST00000558089.1	n.316+129G>T		intron_variant	Intron 2 of 3	4
ENSG00000259280	ENST00000561259.2	n.391-533G>T		intron_variant	Intron 1 of 1	3
ENSG00000259280	ENST00000690156.1	n.117-533G>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23355 AN: 151974 Hom.: 1851 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.167 AC: 3 AN: 18 Hom.: 1 AF XY: 0.250 AC XY: 3 AN XY: 12

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.214 AC: 3 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.154 AC: 23388 AN: 152090 Hom.: 1856 Cov.: 32 AF XY: 0.154 AC XY: 11468 AN XY: 74366

African (AFR) AF: 0.163 AC: 6741 AN: 41472

American (AMR) AF: 0.122 AC: 1863 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5170

South Asian (SAS) AF: 0.167 AC: 805 AN: 4816

European-Finnish (FIN) AF: 0.123 AC: 1301 AN: 10560

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10130 AN: 67996

Other (OTH) AF: 0.166 AC: 350 AN: 2104

Alfa AF: 0.152 Hom.: 5907

Bravo AF: 0.153

Asia WGS AF: 0.207 AC: 721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.072
DANN	Benign	0.75
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs12910772; hg19: chr15-37174402;