rs12800508

Positions:

• chr11-107891897-A-G

Variant summary

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

The ENST00000525071.5(SLC35F2):​c.-349+16544T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0493 in 151,754 control chromosomes in the GnomAD database, including 225 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 0.049 (225 hom., cov: 32)
• Consequence: SLC35F2 ENST00000525071.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 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+16544T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0493 AC: 7476 AN: 151636 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0471

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

GnomAD4 genome AF: 0.0493 AC: 7478 AN: 151754 Hom.: 225 Cov.: 32 AF XY: 0.0488 AC XY: 3614 AN XY: 74122

Gnomad4 AFR AF: 0.0130

Gnomad4 AMR AF: 0.0475

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0586

Gnomad4 FIN AF: 0.0417

Gnomad4 NFE AF: 0.0651

Gnomad4 OTH AF: 0.0476

Alfa AF: 0.0585 Hom.: 140

Bravo AF: 0.0475

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12800508; hg19: chr11-107762623;