chr2-62049838-C-T

Variant names:

• chr2-62049838-C-T
• rs10518958
• NM_152516.4:c.462+48856C>T

Variant summary

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

The NM_152516.4(COMMD1):​c.462+48856C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0836 in 152,020 control chromosomes in the GnomAD database, including 704 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 0.084 (704 hom., cov: 32)
• Consequence: COMMD1 NM_152516.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 1 publications found

Genes affected

COMMD1 (HGNC:23024): (copper metabolism domain containing 1) Enables several functions, including phosphatidylinositol-3,4-bisphosphate binding activity; phospholipid binding activity; and protein homodimerization activity. Involved in several processes, including Golgi to plasma membrane transport; negative regulation of protein localization to cell surface; and regulation of cellular protein metabolic process. Acts upstream of or within negative regulation of NF-kappaB transcription factor activity. Located in cytosol; endosome; and nucleoplasm. Part of Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152516.4. 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
	COMMD1	NM_152516.4	MANE Select	c.462+48856C>T		intron	N/A	NP_689729.1	Q8N668-1
	COMMD1	NM_001321781.3		c.264+48856C>T		intron	N/A	NP_001308710.1
	COMMD1	NM_001321782.3		c.264+48856C>T		intron	N/A	NP_001308711.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD1	ENST00000311832.6	TSL:1 MANE Select	c.462+48856C>T		intron	N/A	ENSP00000308236.5	Q8N668-1
	COMMD1	ENST00000897153.1		c.555+48856C>T		intron	N/A	ENSP00000567212.1
	COMMD1	ENST00000897150.1		c.462+48856C>T		intron	N/A	ENSP00000567209.1

Frequencies

GnomAD3 genomes AF: 0.0837 AC: 12713 AN: 151902 Hom.: 704 Cov.: 32

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.0836 AC: 12712 AN: 152020 Hom.: 704 Cov.: 32 AF XY: 0.0842 AC XY: 6257 AN XY: 74306

African (AFR) AF: 0.0366 AC: 1516 AN: 41468

American (AMR) AF: 0.0492 AC: 751 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 360 AN: 3468

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5186

South Asian (SAS) AF: 0.0879 AC: 423 AN: 4814

European-Finnish (FIN) AF: 0.172 AC: 1816 AN: 10534

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7539 AN: 67962

Other (OTH) AF: 0.0897 AC: 189 AN: 2108

Alfa AF: 0.0989 Hom.: 1333

Bravo AF: 0.0707

Asia WGS AF: 0.0380 AC: 134 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.37
PhyloP100		0.22
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: rs10518958; hg19: chr2-62276973;