5-116294307-T-G

Variant names:

• chr5-116294307-T-G
• rs37181
• ENST00000503424.1:n.104+1747T>G

Variant summary

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

The ENST00000508250.5(COMMD10):​n.148+1747T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,848 control chromosomes in the GnomAD database, including 10,314 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 0.34 (10314 hom., cov: 32)
• Consequence: COMMD10 ENST00000508250.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 8 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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508250.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD10	ENST00000503424.1	TSL:5	n.104+1747T>G		intron	N/A
	COMMD10	ENST00000508250.5	TSL:4	n.148+1747T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51377 AN: 151730 Hom.: 10293 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.339 AC: 51445 AN: 151848 Hom.: 10314 Cov.: 32 AF XY: 0.338 AC XY: 25108 AN XY: 74184

African (AFR) AF: 0.567 AC: 23494 AN: 41414

American (AMR) AF: 0.286 AC: 4365 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 819 AN: 3464

East Asian (EAS) AF: 0.422 AC: 2175 AN: 5158

South Asian (SAS) AF: 0.303 AC: 1461 AN: 4818

European-Finnish (FIN) AF: 0.227 AC: 2393 AN: 10546

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15824 AN: 67876

Other (OTH) AF: 0.326 AC: 688 AN: 2108

Alfa AF: 0.237 Hom.: 2516

Bravo AF: 0.354

Asia WGS AF: 0.387 AC: 1343 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.85
PhyloP100		1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs37181; hg19: chr5-115630004;