18-46672032-A-C

Variant names:

• chr18-46672032-A-C
• rs645631
• NM_013305.6:c.*8010T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013305.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA5	NM_013305.6	MANE Select	c.*8010T>G		3_prime_UTR	Exon 7 of 7	NP_037437.2
	ST8SIA5	NM_001307986.2		c.*8010T>G		3_prime_UTR	Exon 8 of 8	NP_001294915.1
	ST8SIA5	NM_001307987.2		c.*8010T>G		3_prime_UTR	Exon 6 of 6	NP_001294916.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA5	ENST00000315087.12	TSL:1 MANE Select	c.*8010T>G		3_prime_UTR	Exon 7 of 7	ENSP00000321343.6
	ST8SIA5	ENST00000538168.5	TSL:2	c.*8010T>G		3_prime_UTR	Exon 8 of 8	ENSP00000445492.1

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0581 AC: 2414 AN: 41572

American (AMR) AF: 0.177 AC: 2705 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1160 AN: 3466

East Asian (EAS) AF: 0.0655 AC: 339 AN: 5176

South Asian (SAS) AF: 0.107 AC: 519 AN: 4828

European-Finnish (FIN) AF: 0.334 AC: 3535 AN: 10582

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18719 AN: 67992

Other (OTH) AF: 0.215 AC: 453 AN: 2106

Alfa AF: 0.133 Hom.: 223

Bravo AF: 0.183

Asia WGS AF: 0.0820 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.77
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs645631; hg19: chr18-44251995;