chr1-76573600-G-A

Variant names:

• chr1-76573600-G-A
• rs315023
• NM_152996.4:c.624-53852G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001349111.2(ST6GALNAC3):​c.660-53852G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,544 control chromosomes in the GnomAD database, including 13,452 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 0.38 (13452 hom., cov: 31)
• Consequence: ST6GALNAC3 NM_001349111.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001349111.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC3	NM_152996.4	MANE Select	c.624-53852G>A		intron	N/A	NP_694541.2
	ST6GALNAC3	NM_001349111.2		c.660-53852G>A		intron	N/A	NP_001336040.1
	ST6GALNAC3	NM_001349107.2		c.624-55020G>A		intron	N/A	NP_001336036.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ST6GALNAC3	ENST00000328299.4	TSL:1 MANE Select	c.624-53852G>A		intron	N/A	ENSP00000329214.3
	ST6GALNAC3	ENST00000464140.1	TSL:1	n.498-3246G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57834 AN: 151426 Hom.: 13411 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.382 AC: 57922 AN: 151544 Hom.: 13452 Cov.: 31 AF XY: 0.380 AC XY: 28127 AN XY: 74022

African (AFR) AF: 0.664 AC: 27450 AN: 41314

American (AMR) AF: 0.345 AC: 5254 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3466

East Asian (EAS) AF: 0.261 AC: 1345 AN: 5144

South Asian (SAS) AF: 0.264 AC: 1269 AN: 4808

European-Finnish (FIN) AF: 0.272 AC: 2847 AN: 10452

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17264 AN: 67836

Other (OTH) AF: 0.380 AC: 802 AN: 2108

Alfa AF: 0.304 Hom.: 2560

Bravo AF: 0.404

Asia WGS AF: 0.319 AC: 1111 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.044
DANN	Benign	0.20
PhyloP100		-1.2
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: rs315023; hg19: chr1-77039285;