1-76412471-C-T

Variant names:

• chr1-76412471-C-T
• rs17098942
• NM_152996.4:c.623+54C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.81).
• 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 rank	MANE	Protein	UniProt
ST6GALNAC3	NM_152996.4	c.623+54C>T		intron_variant	Intron 3 of 4	ENST00000328299.4	NP_694541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.623+54C>T		intron_variant	Intron 3 of 4	1	NM_152996.4	ENSP00000329214.3
ST6GALNAC3	ENST00000464140.1	n.497+54C>T		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.0933 AC: 2766 AN: 29646

American (AMR) AF: 0.211 AC: 6015 AN: 28574

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 4121 AN: 20622

East Asian (EAS) AF: 0.409 AC: 15711 AN: 38458

South Asian (SAS) AF: 0.408 AC: 28553 AN: 69992

European-Finnish (FIN) AF: 0.238 AC: 10848 AN: 45520

Middle Eastern (MID) AF: 0.247 AC: 1309 AN: 5310

European-Non Finnish (NFE) AF: 0.235 AC: 247755 AN: 1054134

Other (OTH) AF: 0.244 AC: 13620 AN: 55780

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

African (AFR) AF: 0.0982 AC: 4068 AN: 41440

American (AMR) AF: 0.202 AC: 3074 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2067 AN: 5128

South Asian (SAS) AF: 0.432 AC: 2069 AN: 4794

European-Finnish (FIN) AF: 0.237 AC: 2502 AN: 10556

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16249 AN: 67910

Other (OTH) AF: 0.223 AC: 472 AN: 2114

Alfa AF: 0.221 Hom.: 6576

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
PhyloP100		0.94
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: rs17098942; hg19: chr1-76878156; COSMIC: COSV60324941;