rs1335515

Variant names:

• chr14-57918647-T-C
• rs1335515
• ENST00000556568.1:n.282+63266A>G

Variant summary

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

The ENST00000556568.1(SLC35F4):​n.282+63266A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,054 control chromosomes in the GnomAD database, including 4,444 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 0.21 (4444 hom., cov: 32)
• Consequence: SLC35F4 ENST00000556568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 12 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35F4	XM_011536723.4	c.64+63266A>G		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+63266A>G		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32180 AN: 151936 Hom.: 4440 Cov.: 32

Gnomad AFR AF: 0.0590

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.212 AC: 32176 AN: 152054 Hom.: 4444 Cov.: 32 AF XY: 0.210 AC XY: 15599 AN XY: 74340

African (AFR) AF: 0.0589 AC: 2441 AN: 41466

American (AMR) AF: 0.200 AC: 3059 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 705 AN: 3470

East Asian (EAS) AF: 0.0126 AC: 65 AN: 5174

South Asian (SAS) AF: 0.220 AC: 1056 AN: 4810

European-Finnish (FIN) AF: 0.295 AC: 3118 AN: 10582

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21019 AN: 67952

Other (OTH) AF: 0.200 AC: 422 AN: 2114

Alfa AF: 0.262 Hom.: 11347

Bravo AF: 0.197

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1335515; hg19: chr14-58385365;