1-99997304-T-C

Position:

• chr1-99997304-T-C

Variant summary

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

The NM_012243.3(SLC35A3):​c.188-1957T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 150,002 control chromosomes in the GnomAD database, including 7,187 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 0.25 (7187 hom., cov: 28)
• Consequence: SLC35A3 NM_012243.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

SLC35A3 (HGNC:11023): (solute carrier family 35 member A3) This gene encodes a UDP-N-acetylglucosamine transporter found in the golgi apparatus membrane. In cattle, a missense mutation in this gene causes complex vertebral malformation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

ENSG00000283761 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35A3	NM_012243.3	c.188-1957T>C		intron_variant		ENST00000533028.8	NP_036375.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35A3	ENST00000533028.8	c.188-1957T>C		intron_variant		1	NM_012243.3	ENSP00000433849.1
ENSG00000283761	ENST00000639037.1	c.188-1957T>C		intron_variant		5		ENSP00000492745.1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37272 AN: 149898 Hom.: 7159 Cov.: 28

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.249 AC: 37342 AN: 150002 Hom.: 7187 Cov.: 28 AF XY: 0.242 AC XY: 17692 AN XY: 73160

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0555

Gnomad4 SAS AF: 0.0976

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.216

Alfa AF: 0.165 Hom.: 1513

Bravo AF: 0.265

Asia WGS AF: 0.133 AC: 463 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.8
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: rs7530361; hg19: chr1-100462860;