11-107799502-T-C

Variant names:

• chr11-107799502-T-C
• rs500063
• NM_017515.5:c.939+3499A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017515.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F2	NM_017515.5	MANE Select	c.939+3499A>G		intron	N/A	NP_059985.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F2	ENST00000525815.6	TSL:1 MANE Select	c.939+3499A>G		intron	N/A	ENSP00000436785.1
	SLC35F2	ENST00000525071.5	TSL:2	c.939+3499A>G		intron	N/A	ENSP00000434307.1
	SLC35F2	ENST00000375682.8	TSL:5	c.798+3499A>G		intron	N/A	ENSP00000364834.4

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

African (AFR) AF: 0.486 AC: 20152 AN: 41474

American (AMR) AF: 0.401 AC: 6121 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1666 AN: 3466

East Asian (EAS) AF: 0.254 AC: 1314 AN: 5172

South Asian (SAS) AF: 0.480 AC: 2309 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5302 AN: 10550

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36348 AN: 67900

Other (OTH) AF: 0.471 AC: 993 AN: 2108

Alfa AF: 0.520 Hom.: 70886

Bravo AF: 0.483

Asia WGS AF: 0.352 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.68
PhyloP100		0.19
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: rs500063; hg19: chr11-107670228;