14-57583363-CTGAT-CTGATTGAT

Variant names:

• chr14-57583363-C-CTGAT
• rs2308163
• NM_001306087.2:c.588-1934_588-1931dupATCA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001306087.2(SLC35F4):​c.588-1934_588-1931dupATCA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (29577 hom., cov: 0)
• Consequence: SLC35F4 NM_001306087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 6 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]

SLC35F4-AS1 (HGNC:58292):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001306087.2. 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
	SLC35F4	NM_001306087.2	MANE Select	c.588-1934_588-1931dupATCA		intron	N/A	NP_001293016.1	G3V4Z9
	SLC35F4	NM_001206920.2		c.585-1934_585-1931dupATCA		intron	N/A	NP_001193849.1
	SLC35F4	NM_001352015.3		c.579-1934_579-1931dupATCA		intron	N/A	NP_001338944.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35F4	ENST00000556826.6	TSL:5 MANE Select	c.588-1931_588-1930insATCA		intron	N/A	ENSP00000452086.1	G3V4Z9
	SLC35F4	ENST00000554729.5	TSL:1	c.219-1931_219-1930insATCA		intron	N/A	ENSP00000451990.1	A4IF30-2
	SLC35F4	ENST00000557254.5	TSL:1	n.219-1931_219-1930insATCA		intron	N/A	ENSP00000450836.1	G3V2S4

Frequencies

GnomAD3 genomes AF: 0.620 AC: 93846 AN: 151412 Hom.: 29553 Cov.: 0

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.620 AC: 93912 AN: 151530 Hom.: 29577 Cov.: 0 AF XY: 0.626 AC XY: 46301 AN XY: 74004

African (AFR) AF: 0.666 AC: 27477 AN: 41278

American (AMR) AF: 0.540 AC: 8232 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3470

East Asian (EAS) AF: 0.873 AC: 4473 AN: 5122

South Asian (SAS) AF: 0.631 AC: 3037 AN: 4816

European-Finnish (FIN) AF: 0.704 AC: 7383 AN: 10480

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39550 AN: 67816

Other (OTH) AF: 0.621 AC: 1311 AN: 2110

Alfa AF: 0.591 Hom.: 2897

Asia WGS AF: 0.701 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.090
Mutation Taster		=100/0	polymorphism (auto)

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: rs2308163;

hg19: chr14-58050081;