rs2186903

Positions:

• chr11-107885825-G-A
• chr11-107885825-G-T

Variant summary

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

The ENST00000525071.5(SLC35F2):​c.-349+22616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 150,204 control chromosomes in the GnomAD database, including 3,540 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 0.19 (3540 hom., cov: 30)
• Consequence: SLC35F2 ENST00000525071.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F2	ENST00000525071.5	c.-349+22616C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 27963 AN: 150146 Hom.: 3526 Cov.: 30

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.186 AC: 27990 AN: 150204 Hom.: 3540 Cov.: 30 AF XY: 0.196 AC XY: 14305 AN XY: 73098

Gnomad4 AFR AF: 0.0420

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.229

Alfa AF: 0.203 Hom.: 1788

Bravo AF: 0.190

Asia WGS AF: 0.267 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2186903; hg19: chr11-107756551;