3-112579498-A-G

Position:

• chr3-112579498-A-G

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC35A5	NM_017945.5	c.429-1048A>G		intron_variant		ENST00000492406.6	NP_060415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35A5	ENST00000492406.6	c.429-1048A>G		intron_variant		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

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.986

Gnomad4 ASJ AF: 0.993

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.990

Gnomad4 OTH AF: 0.964

Alfa AF: 0.985 Hom.: 67390

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

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: rs1472107; hg19: chr3-112298345;