rs144280370

Variant names:

• chr3-112580649-C-A
• rs144280370
• NM_017945.5:c.532C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-112580649-C-A
• chr3-112580649-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_017945.5(SLC35A5):​c.532C>A​(p.Arg178Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R178C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SLC35A5 NM_017945.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.62

Genes affected

SLC35A5 (HGNC:20792): (solute carrier family 35 member A5) This gene encodes a transmembrane protein which belongs to subfamily 35A of the solute carrier superfamily. The encoded protein is a nucleoside-sugar transporter. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.15993932).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A5	NM_017945.5	c.532C>A	p.Arg178Ser	missense_variant	Exon 6 of 7	ENST00000492406.6	NP_060415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35A5	ENST00000492406.6	c.532C>A	p.Arg178Ser	missense_variant	Exon 6 of 7	1	NM_017945.5	ENSP00000417654.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.51
CADD	Benign	22
DANN	Benign	0.91
DEOGEN2	Benign	0.067	T;.;.
Eigen	Benign	-0.19
Eigen_PC	Benign	0.039
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.61	T;T;T
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.16	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.34	N;.;.
PrimateAI	Benign	0.27	T
PROVEAN	Benign	-0.14	N;N;N
REVEL	Benign	0.085
Sift	Benign	0.22	T;T;T
Sift4G	Benign	0.49	T;T;T
Polyphen		0.0020	B;.;.
Vest4		0.27
MutPred		0.53		Gain of glycosylation at R178 (P = 0.003);Gain of glycosylation at R178 (P = 0.003);.;
MVP		0.57
MPC		0.17
ClinPred		0.67	D
GERP RS		5.8
Varity_R		0.28
gMVP		0.39

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: rs144280370; hg19: chr3-112299496; COSMIC: COSV53727041; COSMIC: COSV53727041;