18-46672311-G-T

Position:

• chr18-46672311-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.*7731C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,054 control chromosomes in the GnomAD database, including 3,486 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 0.21 (3486 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ST8SIA5 NM_013305.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST8SIA5	NM_013305.6	c.*7731C>A		3_prime_UTR_variant	7/7	ENST00000315087.12
ST8SIA5	NM_001307986.2	c.*7731C>A		3_prime_UTR_variant	8/8
ST8SIA5	NM_001307987.2	c.*7731C>A		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST8SIA5	ENST00000315087.12	c.*7731C>A		3_prime_UTR_variant	7/7	1	NM_013305.6	P4
ST8SIA5	ENST00000538168.5	c.*7731C>A		3_prime_UTR_variant	8/8	2		A1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31498 AN: 151936 Hom.: 3487 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.207 AC: 31509 AN: 152054 Hom.: 3486 Cov.: 32 AF XY: 0.208 AC XY: 15430 AN XY: 74326

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.185

Alfa AF: 0.228 Hom.: 5635

Bravo AF: 0.204

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073744; hg19: chr18-44252274;