chr19-51293045-T-C

Variant names:

• chr19-51293045-T-C
• rs10414689
• ENST00000601044.2:n.1031-725T>C

Variant summary

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

The ENST00000601044.2(SIGLEC24P):​n.1031-725T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,224 control chromosomes in the GnomAD database, including 2,611 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 (2611 hom., cov: 32)
• Consequence: SIGLEC24P ENST00000601044.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 5 publications found

Genes affected

SIGLEC24P (HGNC:15613): (sialic acid binding Ig like lectin 24, pseudogene)

ENSG00000299241 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 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
SIGLEC24P	ENST00000601044.2	n.1031-725T>C		intron_variant	Intron 4 of 5	6
ENSG00000299241	ENST00000761902.1	n.-239T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16392 AN: 152106 Hom.: 2593 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.000282

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.108 AC: 16466 AN: 152224 Hom.: 2611 Cov.: 32 AF XY: 0.105 AC XY: 7851 AN XY: 74452

African (AFR) AF: 0.352 AC: 14592 AN: 41482

American (AMR) AF: 0.0469 AC: 717 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3468

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5188

South Asian (SAS) AF: 0.0376 AC: 181 AN: 4820

European-Finnish (FIN) AF: 0.000282 AC: 3 AN: 10622

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 688 AN: 68026

Other (OTH) AF: 0.0823 AC: 174 AN: 2114

Alfa AF: 0.0935 Hom.: 1958

Bravo AF: 0.121

Asia WGS AF: 0.0820 AC: 287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.44
DANN	Benign	0.15
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10414689; hg19: chr19-51796299;