18-46672032-A-C

Position:

• chr18-46672032-A-C

Variant summary

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

The NM_013305.6(ST8SIA5):​c.*8010T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,214 control chromosomes in the GnomAD database, including 3,847 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 0.20 (3847 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ST8SIA5 NM_013305.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST8SIA5	NM_013305.6	c.*8010T>G		3_prime_UTR_variant	7/7	ENST00000315087.12
ST8SIA5	NM_001307986.2	c.*8010T>G		3_prime_UTR_variant	8/8
ST8SIA5	NM_001307987.2	c.*8010T>G		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST8SIA5	ENST00000315087.12	c.*8010T>G		3_prime_UTR_variant	7/7	1	NM_013305.6	P4
ST8SIA5	ENST00000538168.5	c.*8010T>G		3_prime_UTR_variant	8/8	2		A1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30187 AN: 152096 Hom.: 3849 Cov.: 33

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.0653

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.217

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.198 AC: 30178 AN: 152214 Hom.: 3847 Cov.: 33 AF XY: 0.199 AC XY: 14822 AN XY: 74412

Gnomad4 AFR AF: 0.0581

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.0655

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.215

Alfa AF: 0.135 Hom.: 218

Bravo AF: 0.183

Asia WGS AF: 0.0820 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs645631; hg19: chr18-44251995;