Genetic Variant APOBEC3H:p.Gly105Ser (chr22-39101399-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001166003.3(APOBEC3H):c.313G>A(p.Gly105Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict 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. G105V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 22)

Consequence

APOBEC3H
NM_001166003.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65

Publications

68 publications found

Variant links:

Genes affected

APOBEC3H (HGNC:24100): (apolipoprotein B mRNA editing enzyme catalytic subunit 3H) This gene encodes a member of the apolipoprotein B mRNA-editing enzyme catalytic polypeptide 3 family of proteins. The encoded protein is a cytidine deaminase that has antiretroviral activity by generating lethal hypermutations in viral genomes. Polymorphisms and alternative splicing in this gene influence its antiretroviral activity and are associated with increased resistence to human immunodeficiency virus type 1 infection in certain populations. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

APOBEC3H links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.07257208).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166003.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
APOBEC3H	NM_181773.5	MANE Select	c.313G>A	p.Gly105Ser	missense	Exon 3 of 5	NP_861438.3
APOBEC3H	NM_001166003.3		c.313G>A	p.Gly105Ser	missense	Exon 3 of 6	NP_001159475.2
APOBEC3H	NM_001166002.3		c.313G>A	p.Gly105Ser	missense	Exon 3 of 5	NP_001159474.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
APOBEC3H	ENST00000442487.8	TSL:3 MANE Select	c.313G>A	p.Gly105Ser	missense	Exon 3 of 5	ENSP00000411754.3
APOBEC3H	ENST00000348946.8	TSL:1	c.313G>A	p.Gly105Ser	missense	Exon 3 of 5	ENSP00000216123.5
APOBEC3H	ENST00000613996.1	TSL:1	c.313G>A	p.Gly105Ser	missense	Exon 2 of 3	ENSP00000482682.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000398

AC:

AN:

251172

AF XY:

0.00

show subpopulations

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.:

Alfa

AF:

0.00

Hom.:

4607

ExAC

AF:

0.00000824

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.55

CADD

Benign

0.017

(source)

DANN

Benign

0.90

DEOGEN2

Benign

0.0025

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0051

LIST_S2

Benign

0.074

M_CAP

Benign

0.0098

MetaRNN

Benign

0.073

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.2

PhyloP100

-1.6

PrimateAI

Benign

0.22

PROVEAN

Benign

1.7

REVEL

Benign

0.052

Sift

Benign

0.11

Sift4G

Benign

0.077

Vest4

0.055

MutPred

0.39

Gain of glycosylation at G105 (P = 0.0721)

MVP

0.47

MPC

0.18

ClinPred

0.099

GERP RS

-4.6

Varity_R

0.032

gMVP

0.11

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over