rs3011225

Variant names:

• chr1-43853701-G-A
• rs3011225
• NM_006279.5:c.302+15390G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-43853701-G-A
• chr1-43853701-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006279.5(ST3GAL3):​c.302+15390G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,154 control chromosomes in the GnomAD database, including 31,455 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 0.60 (31455 hom., cov: 32)
• Consequence: ST3GAL3 NM_006279.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.971

Genes affected

ST3GAL3 (HGNC:10866): (ST3 beta-galactoside alpha-2,3-sialyltransferase 3) The protein encoded by this gene is a type II membrane protein that catalyzes the transfer of sialic acid from CMP-sialic acid to galactose-containing substrates. The encoded protein is normally found in the Golgi apparatus but can be proteolytically processed to a soluble form. This protein is a member of glycosyltransferase family 29. Mutations in this gene have been associated with a form of autosomal recessive nonsymdromic cognitive disability as well as infantile epileptic encephalopathy. Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

ENSG00000284989 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ST3GAL3	NM_006279.5	c.302+15390G>A		intron_variant	Intron 5 of 11	ENST00000347631.8	NP_006270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ST3GAL3	ENST00000347631.8	c.302+15390G>A		intron_variant	Intron 5 of 11	5	NM_006279.5	ENSP00000317192.6
ENSG00000284989	ENST00000645057.1	n.*1624+15390G>A		intron_variant	Intron 19 of 25			ENSP00000494063.1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91445 AN: 152036 Hom.: 31451 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.601 AC: 91472 AN: 152154 Hom.: 31455 Cov.: 32 AF XY: 0.599 AC XY: 44526 AN XY: 74388

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.646

Alfa AF: 0.747 Hom.: 91977

Bravo AF: 0.574

Asia WGS AF: 0.638 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs3011225; hg19: chr1-44319373;