rs808225

Variant names:

• chr14-57931198-A-G
• rs808225
• XM_011536723.4:c.64+50715T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000556568.1(SLC35F4):​n.282+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 ENST00000556568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.90
• Publications: 15 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556568.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F4	ENST00000556568.1	TSL:4	n.282+50715T>C		intron	N/A

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

African (AFR) AF: 0.659 AC: 27290 AN: 41434

American (AMR) AF: 0.415 AC: 6345 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2038 AN: 3468

East Asian (EAS) AF: 0.757 AC: 3907 AN: 5160

South Asian (SAS) AF: 0.410 AC: 1973 AN: 4816

European-Finnish (FIN) AF: 0.374 AC: 3945 AN: 10544

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28107 AN: 67952

Other (OTH) AF: 0.518 AC: 1095 AN: 2112

Alfa AF: 0.451 Hom.: 56740

Bravo AF: 0.510

Asia WGS AF: 0.558 AC: 1942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.031
DANN	Benign	0.40
PhyloP100		-3.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs808225;

hg19: chr14-58397916;