20-46358679-C-G

Position:

• chr20-46358679-C-G

Variant summary

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

The NM_015945.12(SLC35C2):​c.-173G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,551,074 control chromosomes in the GnomAD database, including 70,098 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 0.24 (5435 hom., cov: 32)
  • Exomes 𝑓: 0.30 (64663 hom.)
• Consequence: SLC35C2 NM_015945.12 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520

Genes affected

SLC35C2 (HGNC:17117): (solute carrier family 35 member C2) This gene encodes a member of the triose-phosphate transporter protein family. This gene is regulated by oxygen tension, is induced in hypoxic trophoblast cells, and is overexpressed in ovarian cancer. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been defined on the X chromosome. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35C2	NM_015945.12	c.-173G>C		5_prime_UTR_variant	2/10	ENST00000372230.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35C2	ENST00000372230.10	c.-173G>C		5_prime_UTR_variant	2/10	1	NM_015945.12	P1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35974 AN: 152034 Hom.: 5442 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0734

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.228

GnomAD3 exomes AF: 0.287 AC: 44249 AN: 154426 Hom.: 7074 AF XY: 0.287 AC XY: 23614 AN XY: 82280

Gnomad AFR exome AF: 0.0517

Gnomad AMR exome AF: 0.335

Gnomad ASJ exome AF: 0.241

Gnomad EAS exome AF: 0.0688

Gnomad SAS exome AF: 0.282

Gnomad FIN exome AF: 0.389

Gnomad NFE exome AF: 0.315

Gnomad OTH exome AF: 0.291

GnomAD4 exome AF: 0.298 AC: 416749 AN: 1398922 Hom.: 64663 Cov.: 36 AF XY: 0.298 AC XY: 205526 AN XY: 689990

Gnomad4 AFR exome AF: 0.0522

Gnomad4 AMR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.246

Gnomad4 EAS exome AF: 0.0798

Gnomad4 SAS exome AF: 0.281

Gnomad4 FIN exome AF: 0.380

Gnomad4 NFE exome AF: 0.312

Gnomad4 OTH exome AF: 0.268

GnomAD4 genome AF: 0.236 AC: 35955 AN: 152152 Hom.: 5435 Cov.: 32 AF XY: 0.239 AC XY: 17783 AN XY: 74382

Gnomad4 AFR AF: 0.0632

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.0732

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.225

Alfa AF: 0.210 Hom.: 789

Bravo AF: 0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs1044369; hg19: chr20-44987318; COSMIC: COSV54758762; COSMIC: COSV54758762;