rs10519057

Variant names:

• chr15-46505527-C-T
• rs10519057
• ENST00000661853.1:n.45+95174C>T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000661853.1(ENSG00000287704):​n.45+95174C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00858 in 152,122 control chromosomes in the GnomAD database, including 14 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 0.0086 (14 hom., cov: 32)
• Consequence: ENSG00000287704 ENST00000661853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS2: High Homozygotes in GnomAd4 at 14 gene

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
ENSG00000287704	ENST00000661853.1	n.45+95174C>T		intron_variant	Intron 1 of 1
ENSG00000287704	ENST00000686120.1	n.57-72680C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00857 AC: 1303 AN: 152004 Hom.: 14 Cov.: 32

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.00564

Gnomad ASJ AF: 0.000865

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00353

Gnomad FIN AF: 0.0269

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0116

Gnomad OTH AF: 0.00479

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

GnomAD4 genome AF: 0.00858 AC: 1305 AN: 152122 Hom.: 14 Cov.: 32 AF XY: 0.00909 AC XY: 676 AN XY: 74352

Gnomad4 AFR AF: 0.00258

Gnomad4 AMR AF: 0.00564

Gnomad4 ASJ AF: 0.000865

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00374

Gnomad4 FIN AF: 0.0269

Gnomad4 NFE AF: 0.0116

Gnomad4 OTH AF: 0.00474

Alfa AF: 0.00959 Hom.: 1

Bravo AF: 0.00671

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519057; hg19: chr15-46797725;