rs12890287

chr14-57654927-C-T

Variant summary

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

The NM_001306087.2(SLC35F4):c.104-60803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 152,046 control chromosomes in the GnomAD database, including 2,946 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 0.17 (2946 hom., cov: 32)
• Consequence: SLC35F4 NM_001306087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F4	NM_001306087.2	c.104-60803G>A		intron_variant		ENST00000556826.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F4	ENST00000556826.6	c.104-60803G>A		intron_variant		5	NM_001306087.2	P1
SLC35F4	ENST00000556568.1	n.283-50672G>A		intron_variant, non_coding_transcript_variant		4
SLC35F4	ENST00000557430.1	n.97-50672G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.168 AC: 25492 AN: 151928 Hom.: 2934 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0899

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0981

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.168 AC: 25557 AN: 152046 Hom.: 2946 Cov.: 32 AF XY: 0.165 AC XY: 12284 AN XY: 74342

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0899

Gnomad4 NFE AF: 0.0982

Gnomad4 OTH AF: 0.167

Alfa AF: 0.132 Hom.: 347

Bravo AF: 0.179

Asia WGS AF: 0.188 AC: 653 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	8.3
Dann	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12890287; hg19: chr14-58121645;