chr14-57926710-A-T

Variant names:

• chr14-57926710-A-T
• rs1955648
• ENST00000556568.1:n.282+55203T>A

Variant summary

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

The ENST00000556568.1(SLC35F4):​n.282+55203T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0975 in 113,666 control chromosomes in the GnomAD database, including 483 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 0.098 (483 hom., cov: 28)
• Consequence: SLC35F4 ENST00000556568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35F4	XM_011536723.4	c.64+55203T>A		intron_variant	Intron 1 of 7		XP_011535025.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F4	ENST00000556568.1	n.282+55203T>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.0976 AC: 11079 AN: 113572 Hom.: 484 Cov.: 28

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.0975 AC: 11088 AN: 113666 Hom.: 483 Cov.: 28 AF XY: 0.0949 AC XY: 5131 AN XY: 54044

African (AFR) AF: 0.101 AC: 2651 AN: 26326

American (AMR) AF: 0.0745 AC: 805 AN: 10806

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 359 AN: 2908

East Asian (EAS) AF: 0.0134 AC: 41 AN: 3050

South Asian (SAS) AF: 0.0958 AC: 266 AN: 2778

European-Finnish (FIN) AF: 0.0317 AC: 220 AN: 6948

Middle Eastern (MID) AF: 0.157 AC: 38 AN: 242

European-Non Finnish (NFE) AF: 0.108 AC: 6319 AN: 58248

Other (OTH) AF: 0.121 AC: 186 AN: 1534

Alfa AF: 0.0821 Hom.: 69

Bravo AF: 0.0761

Asia WGS AF: 0.0410 AC: 144 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.59
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1955648; hg19: chr14-58393428;