rs759898407

Variant names:

• chr5-116085062-C-A
• NM_016144.4:c.10C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-116085062-C-A
• chr5-116085062-C-G
• chr5-116085062-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.10C>A​(p.Pro4Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000686 in 1,457,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. P4S) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: COMMD10 NM_016144.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

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

ENSG00000271918 (HGNC:):

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=0.041858256).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMMD10	NM_016144.4	c.10C>A	p.Pro4Thr	missense_variant	Exon 1 of 7	ENST00000274458.9	NP_057228.1
COMMD10	NR_146218.2	n.38C>A		non_coding_transcript_exon_variant	Exon 1 of 7
COMMD10	NR_146220.2	n.38C>A		non_coding_transcript_exon_variant	Exon 1 of 8
COMMD10	NR_146219.2	n.-216C>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000274458.9	c.10C>A	p.Pro4Thr	missense_variant	Exon 1 of 7	1	NM_016144.4	ENSP00000274458.4
COMMD10	ENST00000632434	c.-33C>A		5_prime_UTR_variant	Exon 1 of 7	1		ENSP00000488332.1
COMMD10	ENST00000507356.5	n.10C>A		non_coding_transcript_exon_variant	Exon 1 of 7	3		ENSP00000422448.1
ENSG00000271918	ENST00000606662.2	n.383G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.86e-7 AC: 1 AN: 1457084 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 724556

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.065
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.70
CADD	Benign	0.74
DANN	Benign	0.74
DEOGEN2	Benign	0.0022	T
Eigen	Benign	-1.4
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.031	N
LIST_S2	Benign	0.62	T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.042	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	0.69	N
PrimateAI	Uncertain	0.52	T
PROVEAN	Benign	0.62	N
REVEL	Benign	0.032
Sift	Benign	0.30	T
Sift4G	Benign	0.21	T
Polyphen		0.0	B
Vest4		0.13
MutPred		0.15		Gain of helix (P = 0.0425);
MVP		0.072
MPC		0.0056
ClinPred		0.059	T
GERP RS		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.7
Varity_R		0.034
gMVP		0.44

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: chr5-115420759;