rs12800508

Variant names:

• chr11-107891897-A-G
• rs12800508
• ENST00000525071.5:c.-349+16544T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525071.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F2	ENST00000525071.5	TSL:2	c.-349+16544T>C		intron	N/A	ENSP00000434307.1	Q8IXU6-2

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

African (AFR) AF: 0.0130 AC: 539 AN: 41404

American (AMR) AF: 0.0475 AC: 722 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.0874 AC: 303 AN: 3466

East Asian (EAS) AF: 0.107 AC: 554 AN: 5158

South Asian (SAS) AF: 0.0586 AC: 281 AN: 4794

European-Finnish (FIN) AF: 0.0417 AC: 439 AN: 10528

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4420 AN: 67886

Other (OTH) AF: 0.0476 AC: 100 AN: 2102

Alfa AF: 0.0586 Hom.: 152

Bravo AF: 0.0475

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.93
DANN	Benign	0.11
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12800508;

hg19: chr11-107762623;