rs7518943

Positions:

• chr1-99997866-C-A

Variant summary

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

The NM_012243.3(SLC35A3):​c.188-1395C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 151,912 control chromosomes in the GnomAD database, including 5,070 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 0.22 (5070 hom., cov: 30)
• Consequence: SLC35A3 NM_012243.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.923

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]

LOC124904230 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35A3	NM_012243.3	c.188-1395C>A		intron_variant		ENST00000533028.8	NP_036375.1
LOC124904230	XR_007066249.1	n.279+39864G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35A3	ENST00000533028.8	c.188-1395C>A		intron_variant		1	NM_012243.3	ENSP00000433849	P1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33309 AN: 151794 Hom.: 5055 Cov.: 30

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0996

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.220 AC: 33368 AN: 151912 Hom.: 5070 Cov.: 30 AF XY: 0.214 AC XY: 15887 AN XY: 74232

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.0562

Gnomad4 SAS AF: 0.0993

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.197

Alfa AF: 0.183 Hom.: 575

Bravo AF: 0.230

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.39
DANN	Benign	0.27

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: rs7518943; hg19: chr1-100463422;