rs10515353

Variant names:

• chr5-104585969-T-C
• rs10515353
• ENST00000503650.1:n.329-101317A>G

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.329-101317A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,702 control chromosomes in the GnomAD database, including 1,536 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 0.13 (1536 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 3 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 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
ENSG00000251574	ENST00000503650.1	n.329-101317A>G		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000524336.5	n.191-202587A>G		intron_variant	Intron 2 of 2	3
ENSG00000251574	ENST00000671304.1	n.283-42943A>G		intron_variant	Intron 2 of 4
ENSG00000251574	ENST00000718094.1	n.450+29025A>G		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20048 AN: 151584 Hom.: 1533 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0959

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

GnomAD4 genome AF: 0.132 AC: 20074 AN: 151702 Hom.: 1536 Cov.: 32 AF XY: 0.130 AC XY: 9657 AN XY: 74190

African (AFR) AF: 0.197 AC: 8155 AN: 41466

American (AMR) AF: 0.0884 AC: 1343 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 372 AN: 3454

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5176

South Asian (SAS) AF: 0.0938 AC: 453 AN: 4828

European-Finnish (FIN) AF: 0.116 AC: 1224 AN: 10596

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8211 AN: 67676

Other (OTH) AF: 0.0949 AC: 200 AN: 2108

Alfa AF: 0.130 Hom.: 249

Bravo AF: 0.135

Asia WGS AF: 0.0540 AC: 187 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.79
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10515353; hg19: chr5-103921670;