NM_053041.3:c.84+502T>C

Variant names:

• chr20-32742806-A-G
• rs6119279
• NM_053041.3:c.84+502T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_053041.3(COMMD7):​c.84+502T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,836 control chromosomes in the GnomAD database, including 27,763 homozygotes. 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: 𝑓 0.58 (27763 hom., cov: 30)
• Consequence: COMMD7 NM_053041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMMD7	NM_053041.3	c.84+502T>C		intron_variant	Intron 1 of 8	ENST00000278980.11	NP_444269.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD7	ENST00000278980.11	c.84+502T>C		intron_variant	Intron 1 of 8	1	NM_053041.3	ENSP00000278980.6
ENSG00000285382	ENST00000646357.1	c.84+502T>C		intron_variant	Intron 1 of 8			ENSP00000493768.1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87673 AN: 151718 Hom.: 27716 Cov.: 30

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.524

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.578 AC: 87774 AN: 151836 Hom.: 27763 Cov.: 30 AF XY: 0.583 AC XY: 43215 AN XY: 74186

African (AFR) AF: 0.805 AC: 33332 AN: 41430

American (AMR) AF: 0.586 AC: 8931 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1747 AN: 3468

East Asian (EAS) AF: 0.925 AC: 4756 AN: 5142

South Asian (SAS) AF: 0.667 AC: 3209 AN: 4812

European-Finnish (FIN) AF: 0.449 AC: 4741 AN: 10560

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29316 AN: 67864

Other (OTH) AF: 0.523 AC: 1101 AN: 2104

Alfa AF: 0.522 Hom.: 2890

Bravo AF: 0.600

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.43
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

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: rs6119279; hg19: chr20-31330612;