18-46672311-G-T

Variant names:

• chr18-46672311-G-T
• rs1073744
• NM_013305.6:c.*7731C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA5	NM_013305.6	MANE Select	c.*7731C>A		3_prime_UTR	Exon 7 of 7	NP_037437.2
	ST8SIA5	NM_001307986.2		c.*7731C>A		3_prime_UTR	Exon 8 of 8	NP_001294915.1	O15466-2
	ST8SIA5	NM_001307987.2		c.*7731C>A		3_prime_UTR	Exon 6 of 6	NP_001294916.1	F5H8D1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST8SIA5	ENST00000315087.12	TSL:1 MANE Select	c.*7731C>A		3_prime_UTR	Exon 7 of 7	ENSP00000321343.6	O15466-1
	ST8SIA5	ENST00000538168.5	TSL:2	c.*7731C>A		3_prime_UTR	Exon 8 of 8	ENSP00000445492.1	O15466-2

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

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.123 AC: 5112 AN: 41490

American (AMR) AF: 0.251 AC: 3830 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1139 AN: 5156

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4810

European-Finnish (FIN) AF: 0.249 AC: 2632 AN: 10574

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16580 AN: 67960

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.227 Hom.: 7040

Bravo AF: 0.204

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.74
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1073744; hg19: chr18-44252274;