Genetic Variant SLC35F4:c.103+114018T>C (chr14-57751705-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is . The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001306087.2(SLC35F4):c.103+114018T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,212 control chromosomes in the GnomAD database, including 2,887 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 0.18 ( 2887 hom., cov: 32)

Consequence

SLC35F4
NM_001306087.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.590

Publications

1 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:

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new If you want to explore the variant's impact on the transcript NM_001306087.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.26 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC35F4	NM_001306087.2	MANE Select	c.103+114018T>C	intron	N/A	NP_001293016.1	G3V4Z9
SLC35F4	NM_001206920.2		c.103+114018T>C	intron	N/A	NP_001193849.1
SLC35F4	NM_001352015.3		c.94+113856T>C	intron	N/A	NP_001338944.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC35F4	ENST00000556826.6	TSL:5 MANE Select	c.103+114018T>C	intron	N/A	ENSP00000452086.1	G3V4Z9
SLC35F4	ENST00000556568.1	TSL:4	n.283-147450T>C	intron	N/A
SLC35F4	ENST00000557430.1	TSL:4	n.96+47707T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

27995

AN:

152094

Hom.:

2886

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0908

Gnomad AMI

AF:

0.371

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.226

Gnomad OTH

AF:

0.210

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

GnomAD4 genome

AF:

0.184

AC:

27997

AN:

152212

Hom.:

2887

Cov.:

AF XY:

0.183

AC XY:

13610

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0909

AC:

3779

AN:

41556

American (AMR)

AF:

0.178

AC:

2718

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

824

AN:

3466

East Asian (EAS)

AF:

0.178

AC:

921

AN:

5182

South Asian (SAS)

AF:

0.272

AC:

1309

AN:

4816

European-Finnish (FIN)

AF:

0.209

AC:

2210

AN:

10584

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.226

AC:

15400

AN:

68002

Other (OTH)

AF:

0.207

AC:

438

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1151

2302

3452

4603

5754

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

318

636

954

1272

1590

<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:

0.190

Hom.:

343

Bravo

AF:

0.178

Asia WGS

AF:

0.200

AC:

695

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

7.6

(source)

DANN

Benign

0.80

PhyloP100

0.59

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over