rs2847190

Variant names:

• chr11-107886292-G-A
• rs2847190
• ENST00000525071.5:c.-349+22149C>T

Your query was ambiguous. Multiple possible variants found:

• 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]

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F2	ENST00000525071.5	c.-349+22149C>T		intron_variant	Intron 2 of 10	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;