rs146111323

Variant names:

• chr5-116091122-C-A
• rs146111323
• NM_016144.4:c.176C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-116091122-C-A
• chr5-116091122-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016144.4(COMMD10):​c.176C>A​(p.Ala59Glu) 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. 15/21 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. A59V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: COMMD10 NM_016144.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

Genes affected

COMMD10 (HGNC:30201): (COMM domain containing 10) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03264928).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMMD10	NM_016144.4	c.176C>A	p.Ala59Glu	missense_variant	Exon 3 of 7	ENST00000274458.9	NP_057228.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000274458.9	c.176C>A	p.Ala59Glu	missense_variant	Exon 3 of 7	1	NM_016144.4	ENSP00000274458.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.52
CADD	Benign	10
DANN	Benign	0.40
DEOGEN2	Benign	0.0080	T;T;T;T
Eigen	Benign	-1.0
Eigen_PC	Benign	-0.89
FATHMM_MKL	Benign	0.27	N
LIST_S2	Uncertain	0.89	D;D;.;D
M_CAP	Benign	0.0064	T
MetaRNN	Benign	0.033	T;T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	0.90	L;.;.;.
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-1.0	N;.;N;N
REVEL	Benign	0.077
Sift	Benign	0.65	T;.;T;T
Sift4G	Benign	1.0	T;T;T;T
Polyphen		0.0060	B;.;.;.
Vest4		0.34
MutPred		0.47		Gain of helix (P = 0.0325);.;.;.;
MVP		0.048
MPC		0.0057
ClinPred		0.079	T
GERP RS		1.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.051
gMVP		0.34

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

LitVar

Other links and lift over

dbSNP: rs146111323; hg19: chr5-115426819;