5-116392141-G-T

Variant names:

• chr5-116392141-G-T
• rs7702057
• ENST00000503424.1:n.582-7341G>T

Variant summary

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

The ENST00000503424.1(COMMD10):​n.582-7341G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 150,994 control chromosomes in the GnomAD database, including 2,714 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 0.13 (2714 hom., cov: 31)
• Consequence: COMMD10 ENST00000503424.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 9 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000503424.1	n.582-7341G>T		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19949 AN: 150884 Hom.: 2696 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0233

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.132 AC: 19988 AN: 150994 Hom.: 2714 Cov.: 31 AF XY: 0.129 AC XY: 9498 AN XY: 73624

African (AFR) AF: 0.345 AC: 14162 AN: 41086

American (AMR) AF: 0.0617 AC: 935 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 130 AN: 3448

East Asian (EAS) AF: 0.137 AC: 704 AN: 5144

South Asian (SAS) AF: 0.112 AC: 534 AN: 4754

European-Finnish (FIN) AF: 0.0233 AC: 240 AN: 10298

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0444 AC: 3013 AN: 67818

Other (OTH) AF: 0.116 AC: 242 AN: 2094

Alfa AF: 0.0670 Hom.: 2981

Bravo AF: 0.144

Asia WGS AF: 0.147 AC: 512 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.5
DANN	Benign	0.60
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7702057; hg19: chr5-115727838;