5-116240442-A-G

Variant names:

• chr5-116240442-A-G
• rs17139253
• NM_016144.4:c.511-51075A>G

Variant summary

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

The NM_016144.4(COMMD10):​c.511-51075A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,182 control chromosomes in the GnomAD database, including 1,322 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 0.11 (1322 hom., cov: 32)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMMD10	NM_016144.4	c.511-51075A>G		intron_variant	Intron 5 of 6	ENST00000274458.9	NP_057228.1
COMMD10	NM_001308080.2	c.469-51075A>G		intron_variant	Intron 5 of 6		NP_001295009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000274458.9	c.511-51075A>G		intron_variant	Intron 5 of 6	1	NM_016144.4	ENSP00000274458.4

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16507 AN: 152064 Hom.: 1324 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0560

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0556

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.108 AC: 16508 AN: 152182 Hom.: 1322 Cov.: 32 AF XY: 0.108 AC XY: 8044 AN XY: 74398

African (AFR) AF: 0.220 AC: 9122 AN: 41478

American (AMR) AF: 0.0717 AC: 1096 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3470

East Asian (EAS) AF: 0.176 AC: 913 AN: 5174

South Asian (SAS) AF: 0.0558 AC: 269 AN: 4820

European-Finnish (FIN) AF: 0.0585 AC: 621 AN: 10614

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0556 AC: 3784 AN: 68014

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.0381 Hom.: 59

Bravo AF: 0.118

Asia WGS AF: 0.120 AC: 416 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	5.2
DANN	Benign	0.77
PhyloP100		1.6
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: rs17139253; hg19: chr5-115576139;