rs1001013

Variant names:

• chr5-116266222-A-G
• rs1001013
• NM_016144.4:c.511-25295A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_016144.4(COMMD10):​c.511-25295A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00478 in 151,838 control chromosomes in the GnomAD database, including 7 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 0.0048 (7 hom., cov: 32)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS2: High Homozygotes in GnomAd4 at 7 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016144.4. 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
	COMMD10	NM_016144.4	MANE Select	c.511-25295A>G		intron	N/A	NP_057228.1	Q9Y6G5
	COMMD10	NM_001308080.2		c.469-25295A>G		intron	N/A	NP_001295009.1	D6RJ90

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD10	ENST00000274458.9	TSL:1 MANE Select	c.511-25295A>G		intron	N/A	ENSP00000274458.4	Q9Y6G5
	COMMD10	ENST00000632434.1	TSL:1	c.469-25295A>G		intron	N/A	ENSP00000488332.1	D6RJ90
	COMMD10	ENST00000515539.5	TSL:3	c.469-25295A>G		intron	N/A	ENSP00000427319.1	D6RJ90

Frequencies

GnomAD3 genomes AF: 0.00477 AC: 724 AN: 151720 Hom.: 7 Cov.: 32

Gnomad AFR AF: 0.00385

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00355

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.00497

Gnomad FIN AF: 0.0117

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00450

Gnomad OTH AF: 0.00526

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

GnomAD4 genome AF: 0.00478 AC: 726 AN: 151838 Hom.: 7 Cov.: 32 AF XY: 0.00509 AC XY: 378 AN XY: 74234

African (AFR) AF: 0.00383 AC: 158 AN: 41214

American (AMR) AF: 0.00355 AC: 54 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3470

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5170

South Asian (SAS) AF: 0.00498 AC: 24 AN: 4824

European-Finnish (FIN) AF: 0.0117 AC: 124 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00450 AC: 306 AN: 68004

Other (OTH) AF: 0.00520 AC: 11 AN: 2114

Alfa AF: 0.00476 Hom.: 1

Bravo AF: 0.00401

Asia WGS AF: 0.0110 AC: 39 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.6
DANN	Benign	0.92
PhyloP100		0.12
Mutation Taster		=100/0	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: rs1001013; hg19: chr5-115601919;