rs2847190

Positions:

• chr11-107886292-G-A
• chr11-107886292-G-C

Variant summary

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

The ENST00000525071.5(SLC35F2):​c.-349+22149C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,966 control chromosomes in the GnomAD database, including 28,421 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 0.58 (28421 hom., cov: 32)
• Consequence: SLC35F2 ENST00000525071.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.107886292G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35F2	ENST00000525071.5	c.-349+22149C>T		intron_variant		2		ENSP00000434307.1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88445 AN: 151848 Hom.: 28418 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.582 AC: 88462 AN: 151966 Hom.: 28421 Cov.: 32 AF XY: 0.589 AC XY: 43719 AN XY: 74266

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.619

Alfa AF: 0.676 Hom.: 49390

Bravo AF: 0.563

Asia WGS AF: 0.660 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2847190; hg19: chr11-107757018;