rs253959

Positions:

• chr5-116233060-T-C
• chr5-116233060-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
COMMD10	NM_016144.4	c.511-58457T>C		intron_variant		ENST00000274458.9	NP_057228.1
COMMD10	NM_001308080.2	c.469-58457T>C		intron_variant			NP_001295009.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000274458.9	c.511-58457T>C		intron_variant		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

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.516

Alfa AF: 0.616 Hom.: 22993

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs253959; hg19: chr5-115568757;