rs16960377

Variant names:

• chr18-46673444-G-A
• rs16960377
• NM_013305.6:c.*6598C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-46673444-G-A
• chr18-46673444-G-C
• chr18-46673444-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013305.6(ST8SIA5):​c.*6598C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0703 in 152,052 control chromosomes in the GnomAD database, including 568 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 0.070 (568 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ST8SIA5 NM_013305.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 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.*6598C>T		3_prime_UTR	Exon 7 of 7	NP_037437.2
	ST8SIA5	NM_001307986.2		c.*6598C>T		3_prime_UTR	Exon 8 of 8	NP_001294915.1
	ST8SIA5	NM_001307987.2		c.*6598C>T		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.*6598C>T		3_prime_UTR	Exon 7 of 7	ENSP00000321343.6
	ST8SIA5	ENST00000538168.5	TSL:2	c.*6598C>T		3_prime_UTR	Exon 8 of 8	ENSP00000445492.1

Frequencies

GnomAD3 genomes AF: 0.0703 AC: 10686 AN: 151930 Hom.: 569 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0862

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0594

Gnomad OTH AF: 0.0689

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

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

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0703 AC: 10689 AN: 152046 Hom.: 568 Cov.: 32 AF XY: 0.0732 AC XY: 5439 AN XY: 74304

African (AFR) AF: 0.0619 AC: 2567 AN: 41498

American (AMR) AF: 0.0418 AC: 639 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0579 AC: 201 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1663 AN: 5068

South Asian (SAS) AF: 0.104 AC: 501 AN: 4818

European-Finnish (FIN) AF: 0.0862 AC: 914 AN: 10598

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0594 AC: 4040 AN: 67986

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0621 Hom.: 77

Bravo AF: 0.0668

Asia WGS AF: 0.209 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.77
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs16960377; hg19: chr18-44253407;