Genetic Variant SLC35F4:c.588-1934_588-1931dupATCA (chr14-57583363-C-CTGAT) – ACMG Classification: Benign (-8 pts)

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0900

Publications

6 publications found

Variant links:

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 links:

SLC35F4-AS1 (HGNC:58292):

SLC35F4-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35F4	NM_001306087.2 link	c.588-1934_588-1931dupATCA		intron_variant	Intron 3 of 7	ENST00000556826.6	NP_001293016.1	A4IF30G3V4Z9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F4	ENST00000556826.6 link	c.588-1931_588-1930insATCA		intron_variant	Intron 3 of 7	5	NM_001306087.2	ENSP00000452086.1		G3V4Z9

Frequencies

GnomAD3 genomes

AF:

0.620

AC:

93846

AN:

151412

Hom.:

29553

Cov.:

show subpopulations

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.:

AF XY:

0.626

AC XY:

46301

AN XY:

74004

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1787

3574

5360

7147

8934

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

774

1548

2322

3096

3870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.591

Hom.:

2897

Asia WGS

AF:

0.701

AC:

2437

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.090

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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14-57583363-CTGAT-CTGATTGAT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over