15-36057645-T-C

Variant names:

• chr15-36057645-T-C
• rs1898036
• ENST00000561394.1:n.137-24390A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561394.1(ENSG00000259639):​n.137-24390A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0877 in 152,242 control chromosomes in the GnomAD database, including 852 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 0.088 (852 hom., cov: 32)
• Consequence: ENSG00000259639 ENST00000561394.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

ENSG00000259639 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259639	ENST00000561394.1	n.137-24390A>G		intron_variant	Intron 2 of 4	3
ENSG00000259639	ENST00000650498.1	n.137-24390A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0878 AC: 13357 AN: 152124 Hom.: 850 Cov.: 32

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0877 AC: 13355 AN: 152242 Hom.: 852 Cov.: 32 AF XY: 0.0932 AC XY: 6939 AN XY: 74414

Gnomad4 AFR AF: 0.0237

Gnomad4 AMR AF: 0.0592

Gnomad4 ASJ AF: 0.0374

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0973 Hom.: 1562

Bravo AF: 0.0701

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.4
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1898036; hg19: chr15-36349846;