rs808225

Positions:

• chr14-57931198-A-G

Variant summary

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

The XM_011536723.4(SLC35F4):​c.64+50715T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,964 control chromosomes in the GnomAD database, including 19,888 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 0.50 (19888 hom., cov: 32)
• Consequence: SLC35F4 XM_011536723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.90

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35F4	XM_011536723.4	c.64+50715T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F4	ENST00000556568.1	n.282+50715T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75273 AN: 151846 Hom.: 19861 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.496 AC: 75357 AN: 151964 Hom.: 19888 Cov.: 32 AF XY: 0.493 AC XY: 36618 AN XY: 74296

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.518

Alfa AF: 0.444 Hom.: 24332

Bravo AF: 0.510

Asia WGS AF: 0.558 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.031
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs808225; hg19: chr14-58397916;