rs11046430

Variant names:

• chr12-22413495-C-T
• rs11046430
• ENST00000508615.3:n.152+4088C>T

Variant summary

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

The ENST00000536558.5(ST8SIA1):​n.166+23381G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0978 in 151,910 control chromosomes in the GnomAD database, including 791 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 0.098 (791 hom., cov: 32)
• Consequence: ST8SIA1 ENST00000536558.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744

Genes affected

C2CD5-AS1 (HGNC:55961): (C2CD5 antisense RNA 1)

ST8SIA1 (HGNC:10869): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1) Gangliosides are membrane-bound glycosphingolipids containing sialic acid. Ganglioside GD3 is known to be important for cell adhesion and growth of cultured malignant cells. The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to GM3 to produce gangliosides GD3 and GT3. The encoded protein may be found in the Golgi apparatus and is a member of glycosyltransferase family 29. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 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
C2CD5-AS1	ENST00000508615.3	n.152+4088C>T		intron_variant	Intron 1 of 3	5
ST8SIA1	ENST00000536558.5	n.166+23381G>A		intron_variant	Intron 1 of 3	3
C2CD5-AS1	ENST00000661495.1	n.171+4088C>T		intron_variant	Intron 1 of 3
C2CD5-AS1	ENST00000689593.1	n.135+4088C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0978 AC: 14841 AN: 151792 Hom.: 789 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0363

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0610

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0922

Gnomad OTH AF: 0.0824

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

GnomAD4 genome AF: 0.0978 AC: 14857 AN: 151910 Hom.: 791 Cov.: 32 AF XY: 0.0968 AC XY: 7190 AN XY: 74256

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0646

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0364

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0610

Gnomad4 NFE AF: 0.0921

Gnomad4 OTH AF: 0.0867

Alfa AF: 0.101 Hom.: 106

Bravo AF: 0.0980

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11046430; hg19: chr12-22566429;