rs2186903

Variant names:

• chr11-107885825-G-A
• rs2186903
• ENST00000525071.5:c.-349+22616C>T

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F2	ENST00000525071.5	c.-349+22616C>T		intron_variant	Intron 2 of 10	2		ENSP00000434307.1

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;