rs1955648

chr14-57926710-A-T

Variant summary

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

The XM_011536723.4(SLC35F4):c.64+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 XM_011536723.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

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=-0.9).
• 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/exons	MANE	UniProt
SLC35F4	XM_011536723.4	c.64+55203T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35F4	ENST00000556568.1	n.282+55203T>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0745

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0134

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.0317

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.121

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1955648; hg19: chr14-58393428;