rs1745689

chr14-57604174-T-Cchr14-57604174-T-G

Variant summary

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

The NM_001306087.2(SLC35F4):c.104-10050A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,052 control chromosomes in the GnomAD database, including 39,296 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 0.71 (39292 hom., cov: 32)
  • Exomes 𝑓: 0.90 (4 hom.)
• Consequence: SLC35F4 NM_001306087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.99

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F4	NM_001306087.2	c.104-10050A>G		intron_variant		ENST00000556826.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F4	ENST00000556826.6	c.104-10050A>G		intron_variant		5	NM_001306087.2	P1
SLC35F4	ENST00000556568.1	n.364A>G		non_coding_transcript_exon_variant	2/2	4
SLC35F4	ENST00000557430.1	n.178A>G		non_coding_transcript_exon_variant	2/4	4

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108183 AN: 151924 Hom.: 39257 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.750

GnomAD4 exome AF: 0.900 AC: 9 AN: 10 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.712 AC: 108279 AN: 152042 Hom.: 39292 Cov.: 32 AF XY: 0.708 AC XY: 52572 AN XY: 74298

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.750

Alfa AF: 0.746 Hom.: 7228

Bravo AF: 0.713

Asia WGS AF: 0.562 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.048
Dann	Benign	0.37

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: rs1745689; hg19: chr14-58070892;