chr1-76133411-A-C

Variant names:

• chr1-76133411-A-C
• rs289698
• NM_152996.4:c.18+58527A>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.18+58527A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0537 in 152,254 control chromosomes in the GnomAD database, including 232 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 0.054 (232 hom., cov: 32)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 2 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 = 0.0709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC3	NM_152996.4	c.18+58527A>C		intron_variant	Intron 1 of 4	ENST00000328299.4	NP_694541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.18+58527A>C		intron_variant	Intron 1 of 4	1	NM_152996.4	ENSP00000329214.3

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 8172 AN: 152136 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.0978

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.0773

Gnomad FIN AF: 0.0757

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0537 AC: 8172 AN: 152254 Hom.: 232 Cov.: 32 AF XY: 0.0547 AC XY: 4077 AN XY: 74470

African (AFR) AF: 0.0557 AC: 2312 AN: 41544

American (AMR) AF: 0.0302 AC: 461 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3470

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5174

South Asian (SAS) AF: 0.0773 AC: 373 AN: 4824

European-Finnish (FIN) AF: 0.0757 AC: 803 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0529 AC: 3599 AN: 68024

Other (OTH) AF: 0.0421 AC: 89 AN: 2112

Alfa AF: 0.0512 Hom.: 443

Bravo AF: 0.0502

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.69
PhyloP100		0.27
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: rs289698; hg19: chr1-76599096;