1-76412471-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152996.4(ST6GALNAC3):c.623+54C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 1,499,866 control chromosomes in the GnomAD database, including 46,420 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 (3831 hom., cov: 32)
  • Exomes 𝑓: 0.25 (42589 hom.)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GALNAC3	NM_152996.4	c.623+54C>T		intron_variant		ENST00000328299.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.623+54C>T		intron_variant		1	NM_152996.4	P1
ST6GALNAC3	ENST00000464140.1	n.497+54C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31426 AN: 151712 Hom.: 3828 Cov.: 32

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.245 AC: 330698 AN: 1348036 Hom.: 42589 AF XY: 0.249 AC XY: 165412 AN XY: 663290

Gnomad4 AFR exome AF: 0.0933

Gnomad4 AMR exome AF: 0.211

Gnomad4 ASJ exome AF: 0.200

Gnomad4 EAS exome AF: 0.409

Gnomad4 SAS exome AF: 0.408

Gnomad4 FIN exome AF: 0.238

Gnomad4 NFE exome AF: 0.235

Gnomad4 OTH exome AF: 0.244

GnomAD4 genome AF: 0.207 AC: 31434 AN: 151830 Hom.: 3831 Cov.: 32 AF XY: 0.213 AC XY: 15771 AN XY: 74178

Gnomad4 AFR AF: 0.0982

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.223

Alfa AF: 0.185 Hom.: 774

Bravo AF: 0.196

Asia WGS AF: 0.391 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.1
Dann	Benign	0.57

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

Publications

LitVar

Other links and lift over

dbSNP: rs17098942; hg19: chr1-76878156; COSMIC: COSV60324941;