chr1-76083548-T-C

Position:

• chr1-76083548-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.18+8664T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,258 control chromosomes in the GnomAD database, including 1,708 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 0.10 (1708 hom., cov: 33)
• Consequence: ST6GALNAC3 NM_152996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

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]

ST6GALNAC3 (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 (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ST6GALNAC3	NM_152996.4	c.18+8664T>C		intron_variant		ENST00000328299.4	NP_694541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ST6GALNAC3	ENST00000328299.4	c.18+8664T>C		intron_variant		1	NM_152996.4	ENSP00000329214.3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15441 AN: 152140 Hom.: 1703 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.102 AC: 15469 AN: 152258 Hom.: 1708 Cov.: 33 AF XY: 0.0991 AC XY: 7376 AN XY: 74450

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.0319

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0867

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.0339

Gnomad4 OTH AF: 0.0704

Alfa AF: 0.0432 Hom.: 433

Bravo AF: 0.108

Asia WGS AF: 0.0640 AC: 224 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	3.4
DANN	Benign	0.74

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: rs11803060; hg19: chr1-76549233;