rs777352425

Variant names:

• chr20-32728132-G-A
• rs777352425
• NM_053041.3:c.95C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-32728132-G-A
• chr20-32728132-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_053041.3(COMMD7):​c.95C>T​(p.Ala32Val) 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. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: COMMD7 NM_053041.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48

Genes affected

COMMD7 (HGNC:16223): (COMM domain containing 7) Enables NF-kappaB binding activity. Involved in negative regulation of NF-kappaB transcription factor activity; negative regulation of transcription, DNA-templated; and tumor necrosis factor-mediated signaling pathway. Predicted to be located in cytoplasmic vesicle. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285382 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22909486).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMMD7	NM_053041.3	c.95C>T	p.Ala32Val	missense_variant	Exon 2 of 9	ENST00000278980.11	NP_444269.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD7	ENST00000278980.11	c.95C>T	p.Ala32Val	missense_variant	Exon 2 of 9	1	NM_053041.3	ENSP00000278980.6
ENSG00000285382	ENST00000646357.1	c.95C>T	p.Ala32Val	missense_variant	Exon 2 of 9			ENSP00000493768.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.097
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.036	.;.;T;.;T
Eigen	Benign	-0.20
Eigen_PC	Benign	-0.094
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Uncertain	0.90	D;D;D;D;D
M_CAP	Benign	0.0081	T
MetaRNN	Benign	0.23	T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.5	.;.;L;.;.
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-1.1	.;.;N;N;.
REVEL	Benign	0.029
Sift	Benign	0.27	.;.;T;T;.
Sift4G	Benign	0.26	.;.;T;T;.
Polyphen		0.21, 0.18	.;.;B;B;.
Vest4		0.24, 0.25
MutPred		0.37		Loss of disorder (P = 0.1572);Loss of disorder (P = 0.1572);Loss of disorder (P = 0.1572);.;Loss of disorder (P = 0.1572);
MVP		0.19
MPC		0.18
ClinPred		0.41	T
GERP RS		3.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.6
Varity_R		0.026
gMVP		0.20

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: rs777352425; hg19: chr20-31315939;