14-57920267-A-C

Position:

• chr14-57920267-A-C

Variant summary

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

The XM_011536723.4(SLC35F4):​c.64+61646T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,056 control chromosomes in the GnomAD database, including 4,480 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 0.24 (4480 hom., cov: 32)
• Consequence: SLC35F4 XM_011536723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35F4	XM_011536723.4	c.64+61646T>G		intron_variant			XP_011535025.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35F4	ENST00000556568.1	n.282+61646T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36488 AN: 151938 Hom.: 4477 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.240 AC: 36531 AN: 152056 Hom.: 4480 Cov.: 32 AF XY: 0.245 AC XY: 18192 AN XY: 74318

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.237

Alfa AF: 0.221 Hom.: 1730

Bravo AF: 0.238

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs811732; hg19: chr14-58386985;