rs1001013

chr5-116266222-A-G

Variant summary

Our verdict is Benign. Variant got -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

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 -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COMMD10	NM_016144.4	c.511-25295A>G		intron_variant		ENST00000274458.9
COMMD10	NM_001308080.2	c.469-25295A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COMMD10	ENST00000274458.9	c.511-25295A>G		intron_variant		1	NM_016144.4	P1

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

Gnomad4 AFR AF: 0.00383

Gnomad4 AMR AF: 0.00355

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.00387

Gnomad4 SAS AF: 0.00498

Gnomad4 FIN AF: 0.0117

Gnomad4 NFE AF: 0.00450

Gnomad4 OTH AF: 0.00520

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	7.6
Dann	Benign	0.92

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: rs1001013; hg19: chr5-115601919;