dbSNP rs117931496: COMMD4P1:n.226C>T (chr15-77941755-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NR_157580.1(COMMD4P1):n.332C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0078 in 1,613,836 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0054 ( 3 hom., cov: 31)

Exomes 𝑓: 0.0080 ( 82 hom. )

Consequence

COMMD4P1
NR_157580.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0290

Publications

0 publications found

Variant links:

Genes affected

COMMD4P1 (HGNC:51909): (COMM domain containing 4 pseudogene 1)

COMMD4P1 links:

ENSG00000290665 (HGNC:):

ENSG00000290665 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 15-77941755-G-A is Benign according to our data. Variant chr15-77941755-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 1879301.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 3 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_157580.1. 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
	COMMD4P1	NR_157580.1		n.332C>T		non_coding_transcript_exon	Exon 4 of 5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
COMMD4P1	ENST00000563867.5	TSL:6	n.226C>T	non_coding_transcript_exon	Exon 4 of 5
ENSG00000290665	ENST00000724229.1		n.350C>T	non_coding_transcript_exon	Exon 4 of 7
ENSG00000290665	ENST00000567226.2	TSL:5	n.411+370C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00545

AC:

829

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00215

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00464

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00862

Gnomad OTH

AF:

0.00621

GnomAD2 exomes

AF:

0.00611

AC:

1534

AN:

251068

AF XY:

0.00612

show subpopulations

Gnomad AFR exome

AF:

0.00166

Gnomad AMR exome

AF:

0.00425

Gnomad ASJ exome

AF:

0.0118

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00120

Gnomad NFE exome

AF:

0.00937

Gnomad OTH exome

AF:

0.00751

GnomAD4 exome

AF:

0.00804

AC:

11755

AN:

1461554

Hom.:

Cov.:

AF XY:

0.00792

AC XY:

5756

AN XY:

727098

show subpopulations

African (AFR)

AF:

0.00134

AC:

AN:

33472

American (AMR)

AF:

0.00441

AC:

197

AN:

44710

Ashkenazi Jewish (ASJ)

AF:

0.0116

AC:

303

AN:

26130

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39698

South Asian (SAS)

AF:

0.00308

AC:

266

AN:

86236

European-Finnish (FIN)

AF:

0.00238

AC:

127

AN:

53408

Middle Eastern (MID)

AF:

0.00645

AC:

AN:

5732

European-Non Finnish (NFE)

AF:

0.00928

AC:

10315

AN:

1111800

Other (OTH)

AF:

0.00769

AC:

464

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

731

1463

2194

2926

3657

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

372

744

1116

1488

1860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00544

AC:

829

AN:

152282

Hom.:

Cov.:

AF XY:

0.00486

AC XY:

362

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.00214

AC:

AN:

41556

American (AMR)

AF:

0.00464

AC:

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0118

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5176

South Asian (SAS)

AF:

0.00269

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00132

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00862

AC:

586

AN:

68002

Other (OTH)

AF:

0.00615

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

134

178

223

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00573

Hom.:

Bravo

AF:

0.00588

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

5.4

(source)

DANN

Benign

0.47

PhyloP100

-0.029

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over