rs10515569

Variant names:

• chr5-146352997-T-C
• rs10515569
• ENST00000515598.1:n.403+22346A>G

Variant summary

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

The ENST00000515598.1(ENSG00000250025):​n.403+22346A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,226 control chromosomes in the GnomAD database, including 1,176 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 0.11 (1176 hom., cov: 33)
• Consequence: ENSG00000250025 ENST00000515598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

ENSG00000250025 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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
ENSG00000250025	ENST00000515598.1	n.403+22346A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16869 AN: 152108 Hom.: 1164 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0341

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0837

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.111 AC: 16920 AN: 152226 Hom.: 1176 Cov.: 33 AF XY: 0.109 AC XY: 8122 AN XY: 74432

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0348

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.0837

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0883 Hom.: 942

Bravo AF: 0.115

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.094
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515569; hg19: chr5-145732560;