chr1-76266222-G-A

Variant names:

• chr1-76266222-G-A
• rs6696780
• NM_152996.4:c.19-47583G>A

Variant summary

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

The NM_152996.4(ST6GALNAC3):​c.19-47583G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,088 control chromosomes in the GnomAD database, including 4,484 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 (4484 hom., cov: 32)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 6 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST6GALNAC3	NM_152996.4	c.19-47583G>A		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.19-47583G>A		intron_variant	Intron 1 of 4	1	NM_152996.4	ENSP00000329214.3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32083 AN: 151970 Hom.: 4479 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.211 AC: 32105 AN: 152088 Hom.: 4484 Cov.: 32 AF XY: 0.207 AC XY: 15401 AN XY: 74332

African (AFR) AF: 0.391 AC: 16194 AN: 41426

American (AMR) AF: 0.143 AC: 2193 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3468

East Asian (EAS) AF: 0.0790 AC: 409 AN: 5174

South Asian (SAS) AF: 0.120 AC: 578 AN: 4820

European-Finnish (FIN) AF: 0.109 AC: 1151 AN: 10596

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9969 AN: 67988

Other (OTH) AF: 0.228 AC: 481 AN: 2110

Alfa AF: 0.177 Hom.: 6921

Bravo AF: 0.225

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.2
DANN	Benign	0.69
PhyloP100		0.73
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: rs6696780; hg19: chr1-76731907;