1-76433779-T-C

Variant names:

• chr1-76433779-T-C
• rs4949718
• NM_152996.4:c.623+21362T>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.623+21362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,844 control chromosomes in the GnomAD database, including 21,780 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 0.52 (21780 hom., cov: 31)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 11 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC3	NM_152996.4	c.623+21362T>C		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+21362T>C		intron_variant	Intron 3 of 4	1	NM_152996.4	ENSP00000329214.3
ST6GALNAC3	ENST00000464140.1	n.497+21362T>C		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78798 AN: 151726 Hom.: 21772 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.519 AC: 78825 AN: 151844 Hom.: 21780 Cov.: 31 AF XY: 0.518 AC XY: 38452 AN XY: 74168

African (AFR) AF: 0.326 AC: 13483 AN: 41386

American (AMR) AF: 0.622 AC: 9496 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1810 AN: 3466

East Asian (EAS) AF: 0.565 AC: 2901 AN: 5132

South Asian (SAS) AF: 0.425 AC: 2048 AN: 4818

European-Finnish (FIN) AF: 0.639 AC: 6721 AN: 10522

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40587 AN: 67934

Other (OTH) AF: 0.510 AC: 1075 AN: 2108

Alfa AF: 0.570 Hom.: 83775

Bravo AF: 0.514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.84
DANN	Benign	0.71
PhyloP100		-0.80
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: rs4949718; hg19: chr1-76899464;