14-57920183-T-A

Position:

• chr14-57920183-T-A

Variant summary

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

The XM_011536723.4(SLC35F4):​c.64+61730A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0226 in 152,306 control chromosomes in the GnomAD database, including 427 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 0.023 (427 hom., cov: 32)
• Consequence: SLC35F4 XM_011536723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887

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=-0.87).
• 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/exons	MANE	Protein	UniProt
SLC35F4	XM_011536723.4	c.64+61730A>T		intron_variant			XP_011535025.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35F4	ENST00000556568.1	n.282+61730A>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0227 AC: 3452 AN: 152188 Hom.: 426 Cov.: 32

Gnomad AFR AF: 0.00338

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00850

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0175

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00967

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0226 AC: 3447 AN: 152306 Hom.: 427 Cov.: 32 AF XY: 0.0248 AC XY: 1848 AN XY: 74476

Gnomad4 AFR AF: 0.00337

Gnomad4 AMR AF: 0.00849

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.0261

Gnomad4 FIN AF: 0.0175

Gnomad4 NFE AF: 0.00967

Gnomad4 OTH AF: 0.0242

Alfa AF: 0.0116 Hom.: 12

Bravo AF: 0.0250

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17093928; hg19: chr14-58386901;