3-112579498-A-G

Variant names:

• chr3-112579498-A-G
• rs1472107
• NM_017945.5:c.429-1048A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017945.5(SLC35A5):​c.429-1048A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 151,874 control chromosomes in the GnomAD database, including 70,410 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 0.96 (70410 hom., cov: 27)
• Consequence: SLC35A5 NM_017945.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A5	NM_017945.5	c.429-1048A>G		intron_variant	Intron 5 of 6	ENST00000492406.6	NP_060415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35A5	ENST00000492406.6	c.429-1048A>G		intron_variant	Intron 5 of 6	1	NM_017945.5	ENSP00000417654.1

Frequencies

GnomAD3 genomes AF: 0.962 AC: 146030 AN: 151756 Hom.: 70378 Cov.: 27

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.986

Gnomad ASJ AF: 0.993

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.964

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

GnomAD4 genome AF: 0.962 AC: 146116 AN: 151874 Hom.: 70410 Cov.: 27 AF XY: 0.963 AC XY: 71493 AN XY: 74218

African (AFR) AF: 0.894 AC: 36983 AN: 41384

American (AMR) AF: 0.986 AC: 15030 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.993 AC: 3447 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5085 AN: 5152

South Asian (SAS) AF: 0.987 AC: 4724 AN: 4786

European-Finnish (FIN) AF: 0.982 AC: 10382 AN: 10570

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67248 AN: 67954

Other (OTH) AF: 0.964 AC: 2029 AN: 2104

Alfa AF: 0.981 Hom.: 88938

Bravo AF: 0.958

Asia WGS AF: 0.973 AC: 3385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1472107; hg19: chr3-112298345;