rs12890287

Variant names:

• chr14-57654927-C-T
• rs12890287
• NM_001306087.2:c.104-60803G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.92).
• 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 rank	MANE	Protein	UniProt
SLC35F4	NM_001306087.2	c.104-60803G>A		intron_variant	Intron 1 of 7	ENST00000556826.6	NP_001293016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F4	ENST00000556826.6	c.104-60803G>A		intron_variant	Intron 1 of 7	5	NM_001306087.2	ENSP00000452086.1
SLC35F4	ENST00000556568.1	n.283-50672G>A		intron_variant	Intron 1 of 1	4
SLC35F4	ENST00000557430.1	n.97-50672G>A		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.327 AC: 13562 AN: 41428

American (AMR) AF: 0.115 AC: 1756 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3468

East Asian (EAS) AF: 0.176 AC: 907 AN: 5148

South Asian (SAS) AF: 0.116 AC: 560 AN: 4816

European-Finnish (FIN) AF: 0.0899 AC: 953 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0982 AC: 6674 AN: 67994

Other (OTH) AF: 0.167 AC: 353 AN: 2108

Alfa AF: 0.137 Hom.: 386

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
PhyloP100		-0.0020
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12890287; hg19: chr14-58121645;