1-76549428-T-C

Variant names:

• chr1-76549428-T-C
• rs172714
• NM_152996.4:c.624-78024T>C

Variant summary

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

The NM_152996.4(ST6GALNAC3):​c.624-78024T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,304 control chromosomes in the GnomAD database, including 2,951 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 (2951 hom., cov: 32)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 0 publications found

Genes affected

ST6GALNAC3 (HGNC:19343): (ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 3) ST6GALNAC3 belongs to a family of sialyltransferases that transfer sialic acids from CMP-sialic acid to terminal positions of carbohydrate groups in glycoproteins and glycolipids (Lee et al., 1999 [PubMed 10207017]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152996.4. 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
	ST6GALNAC3	NM_152996.4	MANE Select	c.624-78024T>C		intron	N/A	NP_694541.2
	ST6GALNAC3	NM_001349111.2		c.660-78024T>C		intron	N/A	NP_001336040.1
	ST6GALNAC3	NM_001349107.2		c.624-79192T>C		intron	N/A	NP_001336036.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC3	ENST00000328299.4	TSL:1 MANE Select	c.624-78024T>C		intron	N/A	ENSP00000329214.3
	ST6GALNAC3	ENST00000464140.1	TSL:1	n.498-27418T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29608 AN: 151212 Hom.: 2954 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.181

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.196 AC: 29614 AN: 151304 Hom.: 2951 Cov.: 32 AF XY: 0.199 AC XY: 14709 AN XY: 73904

African (AFR) AF: 0.212 AC: 8767 AN: 41350

American (AMR) AF: 0.190 AC: 2889 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1054 AN: 5156

South Asian (SAS) AF: 0.241 AC: 1158 AN: 4810

European-Finnish (FIN) AF: 0.227 AC: 2329 AN: 10242

Middle Eastern (MID) AF: 0.132 AC: 38 AN: 288

European-Non Finnish (NFE) AF: 0.180 AC: 12240 AN: 67812

Other (OTH) AF: 0.181 AC: 379 AN: 2094

Alfa AF: 0.178 Hom.: 8186

Bravo AF: 0.193

Asia WGS AF: 0.257 AC: 886 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.71
PhyloP100		0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs172714; hg19: chr1-77015113;