1-3463528-C-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_014448.4(ARHGEF16):​c.444C>T​(p.Asn148Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000757 in 1,320,796 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 7.6e-7 ( 0 hom. )

Consequence

ARHGEF16
NM_014448.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00500
Variant links:
Genes affected
ARHGEF16 (HGNC:15515): (Rho guanine nucleotide exchange factor 16) Although the specific function of this protein is not known yet, it is thought to be involved in protein-protein and protein-lipid interactions. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP7
Synonymous conserved (PhyloP=-0.005 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ARHGEF16NM_014448.4 linkc.444C>T p.Asn148Asn synonymous_variant Exon 2 of 15 ENST00000378378.9 NP_055263.2 Q5VV41-1B3KTS4
ARHGEF16XM_017001049.2 linkc.495C>T p.Asn165Asn synonymous_variant Exon 2 of 15 XP_016856538.1
ARHGEF16XM_017001051.2 linkc.444C>T p.Asn148Asn synonymous_variant Exon 2 of 15 XP_016856540.1 Q5VV41-1
ARHGEF16XM_047418009.1 linkc.495C>T p.Asn165Asn synonymous_variant Exon 2 of 8 XP_047273965.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ARHGEF16ENST00000378378.9 linkc.444C>T p.Asn148Asn synonymous_variant Exon 2 of 15 2 NM_014448.4 ENSP00000367629.4 Q5VV41-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
7.57e-7
AC:
1
AN:
1320796
Hom.:
0
Cov.:
31
AF XY:
0.00000155
AC XY:
1
AN XY:
643100
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000503
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.52
CADD
Benign
3.7
DANN
Benign
0.46
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.4

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-3380092; API