Genetic Variant NM_002167.5: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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002167.5. 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
	ID3	NM_002167.5	MANE Select	c.*271C>T		3_prime_UTR	Exon 3 of 3	NP_002158.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ID3	ENST00000374561.6	TSL:1 MANE Select	c.*271C>T	3_prime_UTR	Exon 3 of 3	ENSP00000363689.5	Q02535
ID3	ENST00000856197.1		c.*264C>T	3_prime_UTR	Exon 3 of 3	ENSP00000526256.1
ID3	ENST00000918746.1		c.*268C>T	3_prime_UTR	Exon 3 of 3	ENSP00000588805.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over