rs1209879

Variant names:

• chr8-144851323-C-A
• rs1209879
• NM_014066.4:c.16G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-144851323-C-A
• chr8-144851323-C-G
• chr8-144851323-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_014066.4(COMMD5):​c.16G>T​(p.Ala6Ser) 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. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: COMMD5 NM_014066.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500
• Publications: 31 publications found

Genes affected

COMMD5 (HGNC:17902): (COMM domain containing 5) Predicted to be involved in proximal tubule morphogenesis. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.043089688).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014066.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD5	NM_014066.4	MANE Select	c.16G>T	p.Ala6Ser	missense	Exon 2 of 2	NP_054785.2
	COMMD5	NM_001081003.3		c.16G>T	p.Ala6Ser	missense	Exon 2 of 2	NP_001074472.1	Q9GZQ3
	COMMD5	NM_001081004.3		c.16G>T	p.Ala6Ser	missense	Exon 2 of 2	NP_001074473.1	Q9GZQ3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD5	ENST00000305103.4	TSL:1 MANE Select	c.16G>T	p.Ala6Ser	missense	Exon 2 of 2	ENSP00000304544.3	Q9GZQ3
	COMMD5	ENST00000402718.4	TSL:1	c.16G>T	p.Ala6Ser	missense	Exon 2 of 2	ENSP00000385793.3	Q9GZQ3
	COMMD5	ENST00000450361.2	TSL:1	c.16G>T	p.Ala6Ser	missense	Exon 2 of 2	ENSP00000394331.2	Q9GZQ3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 48

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.2
DANN	Benign	0.87
DEOGEN2	Benign	0.0011	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.084	N
LIST_S2	Benign	0.53	T
M_CAP	Benign	0.0022	T
MetaRNN	Benign	0.043	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.69	N
PhyloP100		-0.50
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-0.15	N
REVEL	Benign	0.020
Sift	Benign	0.44	T
Sift4G	Benign	0.50	T
Polyphen		0.0030	B
Vest4		0.070
MutPred		0.17		Gain of glycosylation at A6 (P = 0.0053)
MVP		0.23
MPC		0.13
ClinPred		0.025	T
GERP RS		1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.0
Varity_R		0.018
gMVP		0.25
Mutation Taster		=98/2	polymorphism

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

Other links and lift over

dbSNP: rs1209879; hg19: chr8-146076708;