rs1414263

Variant names:

• chr14-57883899-G-A
• rs1414263
• ENST00000556568.1:n.282+98014C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-57883899-G-A
• chr14-57883899-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556568.1(SLC35F4):​n.282+98014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0219 in 151,980 control chromosomes in the GnomAD database, including 425 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 0.022 (425 hom., cov: 32)
• Consequence: SLC35F4 ENST00000556568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 0 publications found

Genes affected

SLC35F4 (HGNC:19845): (solute carrier family 35 member F4) 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35F4	XM_011536723.4	c.64+98014C>T		intron_variant	Intron 1 of 7		XP_011535025.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F4	ENST00000556568.1	n.282+98014C>T		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0219 AC: 3327 AN: 151862 Hom.: 424 Cov.: 32

Gnomad AFR AF: 0.00341

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00755

Gnomad ASJ AF: 0.0309

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.0177

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00859

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0219 AC: 3322 AN: 151980 Hom.: 425 Cov.: 32 AF XY: 0.0239 AC XY: 1776 AN XY: 74270

African (AFR) AF: 0.00340 AC: 141 AN: 41448

American (AMR) AF: 0.00754 AC: 115 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0309 AC: 107 AN: 3468

East Asian (EAS) AF: 0.393 AC: 2033 AN: 5172

South Asian (SAS) AF: 0.0229 AC: 110 AN: 4812

European-Finnish (FIN) AF: 0.0177 AC: 186 AN: 10526

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00859 AC: 584 AN: 67980

Other (OTH) AF: 0.0213 AC: 45 AN: 2110

Alfa AF: 0.0103 Hom.: 10

Bravo AF: 0.0236

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.79
DANN	Benign	0.79
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1414263; hg19: chr14-58350617;