chr1-76549428-T-C

Position:

• chr1-76549428-T-C

Variant summary

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

The NM_152996.4(ST6GALNAC3):​c.624-78024T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 151,304 control chromosomes in the GnomAD database, including 2,951 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 0.20 (2951 hom., cov: 32)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST6GALNAC3	NM_152996.4	c.624-78024T>C		intron_variant		ENST00000328299.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.624-78024T>C		intron_variant		1	NM_152996.4	P1
ST6GALNAC3	ENST00000464140.1	n.498-27418T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29608 AN: 151212 Hom.: 2954 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.196 AC: 29614 AN: 151304 Hom.: 2951 Cov.: 32 AF XY: 0.199 AC XY: 14709 AN XY: 73904

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.181

Alfa AF: 0.170 Hom.: 3565

Bravo AF: 0.193

Asia WGS AF: 0.257 AC: 886 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.71

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: rs172714; hg19: chr1-77015113;