rs10419982

Variant names:

• chr19-51293865-A-G
• rs10419982
• ENST00000601044.2:n.1126A>G

Variant summary

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

The ENST00000761902.1(ENSG00000299241):​n.177A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,054 control chromosomes in the GnomAD database, including 24,281 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 0.56 (24281 hom., cov: 32)
• Consequence: ENSG00000299241 ENST00000761902.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 6 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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761902.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIGLEC24P	ENST00000601044.2	TSL:6	n.1126A>G		non_coding_transcript_exon	Exon 5 of 6
	ENSG00000299241	ENST00000761902.1		n.177A>G		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000299241	ENST00000761903.1		n.151A>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85358 AN: 151936 Hom.: 24271 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.562 AC: 85399 AN: 152054 Hom.: 24281 Cov.: 32 AF XY: 0.559 AC XY: 41575 AN XY: 74336

African (AFR) AF: 0.594 AC: 24648 AN: 41486

American (AMR) AF: 0.448 AC: 6858 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2026 AN: 5146

South Asian (SAS) AF: 0.636 AC: 3066 AN: 4822

European-Finnish (FIN) AF: 0.511 AC: 5407 AN: 10578

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39298 AN: 67940

Other (OTH) AF: 0.560 AC: 1184 AN: 2114

Alfa AF: 0.569 Hom.: 87497

Bravo AF: 0.555

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.0
DANN	Benign	0.90
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs10419982; hg19: chr19-51797119;