1-76306643-T-C

Variant names:

• chr1-76306643-T-C
• rs10873876
• NM_152996.4:c.19-7162T>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.19-7162T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 150,204 control chromosomes in the GnomAD database, including 43,443 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 0.75 (43443 hom., cov: 26)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 18 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC3	NM_152996.4	c.19-7162T>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.19-7162T>C		intron_variant	Intron 1 of 4	1	NM_152996.4	ENSP00000329214.3

Frequencies

GnomAD3 genomes AF: 0.752 AC: 112879 AN: 150094 Hom.: 43413 Cov.: 26

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.721

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.752 AC: 112954 AN: 150204 Hom.: 43443 Cov.: 26 AF XY: 0.752 AC XY: 55077 AN XY: 73198

African (AFR) AF: 0.571 AC: 23319 AN: 40868

American (AMR) AF: 0.782 AC: 11814 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2574 AN: 3458

East Asian (EAS) AF: 0.734 AC: 3694 AN: 5036

South Asian (SAS) AF: 0.823 AC: 3916 AN: 4756

European-Finnish (FIN) AF: 0.822 AC: 8261 AN: 10048

Middle Eastern (MID) AF: 0.717 AC: 208 AN: 290

European-Non Finnish (NFE) AF: 0.841 AC: 56862 AN: 67650

Other (OTH) AF: 0.745 AC: 1553 AN: 2084

Alfa AF: 0.806 Hom.: 154304

Bravo AF: 0.735

Asia WGS AF: 0.798 AC: 2771 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.75
PhyloP100		-0.19
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: rs10873876; hg19: chr1-76772328;