chr5-116233060-T-C

Variant names:

• chr5-116233060-T-C
• rs253959
• NM_016144.4:c.511-58457T>C

Variant summary

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

The NM_016144.4(COMMD10):​c.511-58457T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,986 control chromosomes in the GnomAD database, including 22,074 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 0.49 (22074 hom., cov: 32)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMMD10	NM_016144.4	c.511-58457T>C		intron_variant	Intron 5 of 6	ENST00000274458.9	NP_057228.1
COMMD10	NM_001308080.2	c.469-58457T>C		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.511-58457T>C		intron_variant	Intron 5 of 6	1	NM_016144.4	ENSP00000274458.4

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75163 AN: 151868 Hom.: 22078 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.495 AC: 75167 AN: 151986 Hom.: 22074 Cov.: 32 AF XY: 0.492 AC XY: 36574 AN XY: 74280

African (AFR) AF: 0.161 AC: 6682 AN: 41476

American (AMR) AF: 0.529 AC: 8079 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2138 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2127 AN: 5162

South Asian (SAS) AF: 0.593 AC: 2857 AN: 4816

European-Finnish (FIN) AF: 0.624 AC: 6576 AN: 10546

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44792 AN: 67942

Other (OTH) AF: 0.516 AC: 1087 AN: 2108

Alfa AF: 0.601 Hom.: 75493

Bravo AF: 0.471

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.6
DANN	Benign	0.48
PhyloP100		0.31
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: rs253959; hg19: chr5-115568757;