rs10519041

Variant names:

• chr15-45982821-T-C
• rs10519041
• ENST00000773915.1:n.111+33633T>C

Variant summary

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

The ENST00000773915.1(ENSG00000300769):​n.111+33633T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 151,988 control chromosomes in the GnomAD database, including 4,932 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 0.25 (4932 hom., cov: 32)
• Consequence: ENSG00000300769 ENST00000773915.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697
• Publications: 1 publications found

Genes affected

ENSG00000300769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 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
ENSG00000300769	ENST00000773915.1	n.111+33633T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37518 AN: 151870 Hom.: 4928 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.00905

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.247 AC: 37537 AN: 151988 Hom.: 4932 Cov.: 32 AF XY: 0.244 AC XY: 18122 AN XY: 74282

African (AFR) AF: 0.307 AC: 12733 AN: 41448

American (AMR) AF: 0.178 AC: 2717 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3468

East Asian (EAS) AF: 0.00888 AC: 46 AN: 5180

South Asian (SAS) AF: 0.119 AC: 573 AN: 4820

European-Finnish (FIN) AF: 0.276 AC: 2920 AN: 10566

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16998 AN: 67954

Other (OTH) AF: 0.221 AC: 466 AN: 2112

Alfa AF: 0.247 Hom.: 844

Bravo AF: 0.240

Asia WGS AF: 0.0790 AC: 278 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs10519041; hg19: chr15-46275019;