rs10518987

Variant names:

• chr15-72273446-G-A
• rs10518987
• ENST00000569547.1:n.*29-2342C>T

Variant summary

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

The ENST00000569547.1(ENSG00000273025):​n.*29-2342C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 152,306 control chromosomes in the GnomAD database, including 181 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 0.037 (181 hom., cov: 32)
• Consequence: ENSG00000273025 ENST00000569547.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

Genes affected

ENSG00000273025 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.084 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
ENSG00000273025	ENST00000569547.1	n.*29-2342C>T		intron_variant	Intron 12 of 14	2		ENSP00000454749.1

Frequencies

GnomAD3 genomes AF: 0.0367 AC: 5579 AN: 152188 Hom.: 180 Cov.: 32

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.00762

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0193

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0367 AC: 5597 AN: 152306 Hom.: 181 Cov.: 32 AF XY: 0.0351 AC XY: 2614 AN XY: 74490

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.0156

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.0268

Gnomad4 SAS AF: 0.0103

Gnomad4 FIN AF: 0.00762

Gnomad4 NFE AF: 0.0193

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0208 Hom.: 67

Bravo AF: 0.0398

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518987; hg19: chr15-72565787;