rs495871

chr1-100008900-C-T

Variant summary

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

The NM_012243.3(SLC35A3):c.465+1744C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0588 in 152,280 control chromosomes in the GnomAD database, including 346 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 0.059 (346 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SLC35A3 NM_012243.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35A3	NM_012243.3	c.465+1744C>T		intron_variant		ENST00000533028.8
LOC124904230	XR_007066249.1	n.279+28830G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A3	ENST00000533028.8	c.465+1744C>T		intron_variant		1	NM_012243.3	P1

Frequencies

GnomAD3 genomes AF: 0.0589 AC: 8959 AN: 152160 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0359

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.0154

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0459

Gnomad OTH AF: 0.0511

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.0588 AC: 8959 AN: 152278 Hom.: 346 Cov.: 32 AF XY: 0.0582 AC XY: 4337 AN XY: 74466

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0358

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.0154

Gnomad4 SAS AF: 0.0501

Gnomad4 FIN AF: 0.0403

Gnomad4 NFE AF: 0.0459

Gnomad4 OTH AF: 0.0497

Alfa AF: 0.0495 Hom.: 115

Bravo AF: 0.0580

Asia WGS AF: 0.0350 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.2
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: rs495871; hg19: chr1-100474456;