rs1396485

Variant names:

• chr5-116176655-G-A
• rs1396485
• NM_016144.4:c.510+42477G>A

Variant summary

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

The NM_016144.4(COMMD10):​c.510+42477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,668 control chromosomes in the GnomAD database, including 10,212 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 0.31 (10212 hom., cov: 32)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 7 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

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.510+42477G>A		intron	N/A	NP_057228.1	Q9Y6G5
	COMMD10	NM_001308080.2		c.468+42477G>A		intron	N/A	NP_001295009.1	D6RJ90
	COMMD10	NR_146218.2		n.539-9224G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD10	ENST00000274458.9	TSL:1 MANE Select	c.510+42477G>A		intron	N/A	ENSP00000274458.4	Q9Y6G5
	COMMD10	ENST00000632434.1	TSL:1	c.468+42477G>A		intron	N/A	ENSP00000488332.1	D6RJ90
	COMMD10	ENST00000515539.5	TSL:3	c.468+42477G>A		intron	N/A	ENSP00000427319.1	D6RJ90

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47032 AN: 151550 Hom.: 10189 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.311 AC: 47103 AN: 151668 Hom.: 10212 Cov.: 32 AF XY: 0.309 AC XY: 22872 AN XY: 74106

African (AFR) AF: 0.622 AC: 25729 AN: 41344

American (AMR) AF: 0.263 AC: 4008 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 779 AN: 3464

East Asian (EAS) AF: 0.209 AC: 1075 AN: 5152

South Asian (SAS) AF: 0.144 AC: 693 AN: 4804

European-Finnish (FIN) AF: 0.193 AC: 2027 AN: 10508

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12028 AN: 67866

Other (OTH) AF: 0.286 AC: 605 AN: 2112

Alfa AF: 0.234 Hom.: 12031

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		0.25
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1396485;

hg19: chr5-115512352;