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GeneBe

4-147906644-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_024605.4(ARHGAP10):c.1041C>T(p.Gly347=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00693 in 1,613,932 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 3 hom., cov: 33)
Exomes 𝑓: 0.0072 ( 56 hom. )

Consequence

ARHGAP10
NM_024605.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.07
Variant links:
Genes affected
ARHGAP10 (HGNC:26099): (Rho GTPase activating protein 10) Predicted to enable GTPase activator activity. Predicted to be involved in cytoskeleton organization and negative regulation of apoptotic process. Predicted to be located in perinuclear region of cytoplasm and plasma membrane. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 4-147906644-C-T is Benign according to our data. Variant chr4-147906644-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2655117.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.07 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ARHGAP10NM_024605.4 linkuse as main transcriptc.1041C>T p.Gly347= synonymous_variant 11/23 ENST00000336498.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ARHGAP10ENST00000336498.8 linkuse as main transcriptc.1041C>T p.Gly347= synonymous_variant 11/231 NM_024605.4 P1
ARHGAP10ENST00000506054.5 linkuse as main transcriptn.6173C>T non_coding_transcript_exon_variant 5/171
ARHGAP10ENST00000507661.1 linkuse as main transcriptc.75C>T p.Gly25= synonymous_variant 2/132

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00466
AC:
709
AN:
152042
Hom.:
3
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00126
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00144
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.0107
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00748
Gnomad OTH
AF:
0.00573
GnomAD3 exomes
AF:
0.00458
AC:
1152
AN:
251418
Hom.:
6
AF XY:
0.00470
AC XY:
638
AN XY:
135882
show subpopulations
Gnomad AFR exome
AF:
0.00129
Gnomad AMR exome
AF:
0.00142
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00942
Gnomad NFE exome
AF:
0.00746
Gnomad OTH exome
AF:
0.00408
GnomAD4 exome
AF:
0.00716
AC:
10471
AN:
1461772
Hom.:
56
Cov.:
33
AF XY:
0.00689
AC XY:
5011
AN XY:
727182
show subpopulations
Gnomad4 AFR exome
AF:
0.00122
Gnomad4 AMR exome
AF:
0.00170
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000267
Gnomad4 FIN exome
AF:
0.00959
Gnomad4 NFE exome
AF:
0.00847
Gnomad4 OTH exome
AF:
0.00654
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00466
AC:
709
AN:
152160
Hom.:
3
Cov.:
33
AF XY:
0.00472
AC XY:
351
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.00125
Gnomad4 AMR
AF:
0.00144
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.0107
Gnomad4 NFE
AF:
0.00748
Gnomad4 OTH
AF:
0.00567
Alfa
AF:
0.00551
Hom.:
1
Bravo
AF:
0.00387
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00638
EpiControl
AF:
0.00753

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2022ARHGAP10: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
Cadd
Benign
0.66
Dann
Benign
0.55

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs61748165; hg19: chr4-148827795; API