dbSNP rs2920: ID3:c.*152A>G (chr1-23558289-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002167.5(ID3):c.*152A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,462 control chromosomes in the GnomAD database, including 3,094 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 0.20 ( 3091 hom., cov: 32)

Exomes 𝑓: 0.13 ( 3 hom. )

Consequence

ID3
NM_002167.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.30

Publications

14 publications found

Variant links:

Genes affected

ID3 (HGNC:5362): (inhibitor of DNA binding 3) The protein encoded by this gene is a helix-loop-helix (HLH) protein that can form heterodimers with other HLH proteins. However, the encoded protein lacks a basic DNA-binding domain and therefore inhibits the DNA binding of any HLH protein with which it interacts. [provided by RefSeq, Aug 2011]

ID3 links:

ENSG00000307540 (HGNC:):

ENSG00000307540 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ID3	NM_002167.5 link	c.*152A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000374561.6	NP_002158.3	Q02535
LOC124903876	XR_007065537.1 link	n.282+6194T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ID3	ENST00000374561.6 link	c.*152A>G	3_prime_UTR_variant	Exon 3 of 3	1	NM_002167.5	ENSP00000363689.5	Q02535
ID3	ENST00000463312.1 link	n.268A>G	non_coding_transcript_exon_variant	Exon 2 of 2	2
ENSG00000307540	ENST00000826972.1 link	n.204-14458T>C	intron_variant	Intron 2 of 2
ID3	ENST00000486541.1 link	n.*156A>G	downstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.199

AC:

30244

AN:

152010

Hom.:

3084

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.150

Gnomad EAS

AF:

0.189

Gnomad SAS

AF:

0.0852

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.169

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.193

GnomAD4 exome

AF:

0.129

AC:

AN:

334

Hom.:

Cov.:

AF XY:

0.125

AC XY:

AN XY:

200

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.0833

AC:

AN:

European-Finnish (FIN)

AF:

0.133

AC:

AN:

120

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.137

AC:

AN:

182

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.199

AC:

30291

AN:

152128

Hom.:

3091

Cov.:

AF XY:

0.194

AC XY:

14458

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.212

AC:

8783

AN:

41492

American (AMR)

AF:

0.188

AC:

2867

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.150

AC:

521

AN:

3472

East Asian (EAS)

AF:

0.189

AC:

979

AN:

5168

South Asian (SAS)

AF:

0.0872

AC:

421

AN:

4830

European-Finnish (FIN)

AF:

0.158

AC:

1671

AN:

10590

Middle Eastern (MID)

AF:

0.178

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.212

AC:

14401

AN:

67982

Other (OTH)

AF:

0.191

AC:

403

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1271

2542

3813

5084

6355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.204

Hom.:

12081

Bravo

AF:

0.202

Asia WGS

AF:

0.138

AC:

480

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

(source)

DANN

Benign

0.66

PhyloP100

1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over