rs9952976

Positions:

• chr18-46727756-G-A
• chr18-46727756-G-T

Variant summary

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

The NM_013305.6(ST8SIA5):​c.132-23092C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,006 control chromosomes in the GnomAD database, including 41,930 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 0.74 (41930 hom., cov: 31)
• Consequence: ST8SIA5 NM_013305.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521

Genes affected

ST8SIA5 (HGNC:17827): (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 5) The protein encoded by this gene is a type II membrane protein that may be present in the Golgi apparatus. The encoded protein, which is a member of glycosyltransferase family 29, may be involved in the synthesis of gangliosides GD1c, GT1a, GQ1b, and GT3 from GD1a, GT1b, GM1b, and GD3, respectively. [provided by RefSeq, Jul 2008]

ST8SIA5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST8SIA5	NM_013305.6	c.132-23092C>T		intron_variant		ENST00000315087.12	NP_037437.2
ST8SIA5	NM_001307986.2	c.132-6287C>T		intron_variant			NP_001294915.1
ST8SIA5	NM_001307987.2	c.131+28622C>T		intron_variant			NP_001294916.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST8SIA5	ENST00000315087.12	c.132-23092C>T		intron_variant		1	NM_013305.6	ENSP00000321343.6

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112369 AN: 151888 Hom.: 41880 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.740 AC: 112476 AN: 152006 Hom.: 41930 Cov.: 31 AF XY: 0.744 AC XY: 55300 AN XY: 74304

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.727

Alfa AF: 0.743 Hom.: 84741

Bravo AF: 0.735

Asia WGS AF: 0.894 AC: 3109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9952976; hg19: chr18-44307719;