Genetic Variant ID3:c.*271C>T (chr1-23558170-G-A) – 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.*271C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 152,546 control chromosomes in the GnomAD database, including 33,245 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 0.66 ( 33161 hom., cov: 31)

Exomes 𝑓: 0.57 ( 84 hom. )

Consequence

ID3
NM_002167.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.855

Publications

13 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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ID3	NM_002167.5 link	c.*271C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000374561.6	NP_002158.3	Q02535
LOC124903876	XR_007065537.1 link	n.282+6075G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ID3	ENST00000374561.6 link	c.*271C>T	3_prime_UTR_variant	Exon 3 of 3	1	NM_002167.5	ENSP00000363689.5	Q02535
ID3	ENST00000463312.1 link	n.387C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2
ENSG00000307540	ENST00000826972.1 link	n.204-14577G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.657

AC:

99723

AN:

151880

Hom.:

33131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.690

Gnomad AMI

AF:

0.764

Gnomad AMR

AF:

0.641

Gnomad ASJ

AF:

0.750

Gnomad EAS

AF:

0.925

Gnomad SAS

AF:

0.761

Gnomad FIN

AF:

0.576

Gnomad MID

AF:

0.697

Gnomad NFE

AF:

0.618

Gnomad OTH

AF:

0.681

GnomAD4 exome

AF:

0.566

AC:

309

AN:

546

Hom.:

Cov.:

AF XY:

0.564

AC XY:

185

AN XY:

328

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.555

AC:

243

AN:

438

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.600

AC:

AN:

Other (OTH)

AF:

0.583

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.657

AC:

99810

AN:

152000

Hom.:

33161

Cov.:

AF XY:

0.659

AC XY:

48956

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.690

AC:

28589

AN:

41432

American (AMR)

AF:

0.641

AC:

9800

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

2605

AN:

3472

East Asian (EAS)

AF:

0.925

AC:

4775

AN:

5162

South Asian (SAS)

AF:

0.760

AC:

3660

AN:

4818

European-Finnish (FIN)

AF:

0.576

AC:

6073

AN:

10544

Middle Eastern (MID)

AF:

0.704

AC:

207

AN:

294

European-Non Finnish (NFE)

AF:

0.618

AC:

41977

AN:

67974

Other (OTH)

AF:

0.677

AC:

1429

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1696

3392

5089

6785

8481

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

802

1604

2406

3208

4010

<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:

0.632

Hom.:

101732

Bravo

AF:

0.663

Asia WGS

AF:

0.795

AC:

2764

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

0.85

Mutation Taster

=99/1

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