Genetic Variant NM_025181.5:c.1483C>A (chr2-113719167-G-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_025181.5(SLC35F5):c.1483C>A(p.His495Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H495Q) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

SLC35F5
NM_025181.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 8.11

Variant links:

Genes affected

SLC35F5 (HGNC:23617): (solute carrier family 35 member F5) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC35F5 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35F5	NM_025181.5 link	c.1483C>A	p.His495Asn	missense_variant	Exon 14 of 16	ENST00000245680.7	NP_079457.2	Q8WV83-1A0A024RAD4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35F5	ENST00000245680.7 link	c.1483C>A	p.His495Asn	missense_variant	Exon 14 of 16	1	NM_025181.5	ENSP00000245680.2		Q8WV83-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

243442

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.075

BayesDel_noAF

Benign

-0.35

CADD

Benign

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.0044

T;T

Eigen

Uncertain

0.37

Eigen_PC

Uncertain

0.52

FATHMM_MKL

Pathogenic

1.0

LIST_S2

Uncertain

0.86

D;D

M_CAP

Benign

0.012

MetaRNN

Benign

0.27

T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

0.98

L;.

PhyloP100

8.1

PrimateAI

Uncertain

0.75

PROVEAN

Benign

-0.26

N;.

REVEL

Benign

0.17

Sift

Benign

0.52

T;.

Sift4G

Benign

0.58

T;.

Polyphen

0.90

P;.

Vest4

0.67

MutPred

0.37

Loss of helix (P = 0.0068);.;

MVP

0.59

MPC

0.17

ClinPred

0.65

GERP RS

5.5

Varity_R

0.21

gMVP

0.60

Mutation Taster

=53/47

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.22

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.22

Position offset: -13

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

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