rs500063

Positions:

• chr11-107799502-T-C

Variant summary

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

The NM_017515.5(SLC35F2):​c.939+3499A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,964 control chromosomes in the GnomAD database, including 18,857 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 0.49 (18857 hom., cov: 33)
• Consequence: SLC35F2 NM_017515.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192

Genes affected

SLC35F2 (HGNC:23615): (solute carrier family 35 member F2) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35F2	NM_017515.5	c.939+3499A>G		intron_variant		ENST00000525815.6	NP_059985.2
SLC35F2	XM_047427146.1	c.798+3499A>G		intron_variant			XP_047283102.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35F2	ENST00000525815.6	c.939+3499A>G		intron_variant		1	NM_017515.5	ENSP00000436785	P1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74945 AN: 151846 Hom.: 18852 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.493 AC: 74971 AN: 151964 Hom.: 18857 Cov.: 33 AF XY: 0.486 AC XY: 36069 AN XY: 74276

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.471

Alfa AF: 0.522 Hom.: 33453

Bravo AF: 0.483

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.68

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: rs500063; hg19: chr11-107670228;