dbSNP rs2071495: ENSG00000307540:n.204-14905C>G (chr1-23557842-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000826972.1(ENSG00000307540):n.204-14905C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,704 control chromosomes in the GnomAD database, including 2,112 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 ( 2107 hom., cov: 32)

Exomes 𝑓: 0.12 ( 5 hom. )

Consequence

ENSG00000307540
ENST00000826972.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.155

Publications

5 publications found

Variant links:

Genes affected

ENSG00000307540 (HGNC:):

ENSG00000307540 links:

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:

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903876	XR_007065537.1 link	n.282+5747C>G		intron_variant	Intron 2 of 2
ID3	NM_002167.5 link	c.*599G>C		downstream_gene_variant		ENST00000374561.6	NP_002158.3	Q02535

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ENSG00000307540	ENST00000826972.1 link	n.204-14905C>G	intron_variant	Intron 2 of 2
ID3	ENST00000374561.6 link	c.*599G>C	downstream_gene_variant		1	NM_002167.5	ENSP00000363689.5	Q02535
ID3	ENST00000463312.1 link	n.*92G>C	downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19839

AN:

152136

Hom.:

2112

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0309

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.569

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.175

GnomAD4 exome

AF:

0.124

AC:

AN:

450

Hom.:

AF XY:

0.112

AC XY:

AN XY:

276

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.114

AC:

AN:

422

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.313

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

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:

0.130

AC:

19825

AN:

152254

Hom.:

2107

Cov.:

AF XY:

0.131

AC XY:

9715

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0308

AC:

1281

AN:

41554

American (AMR)

AF:

0.145

AC:

2212

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

887

AN:

3472

East Asian (EAS)

AF:

0.568

AC:

2942

AN:

5180

South Asian (SAS)

AF:

0.107

AC:

515

AN:

4826

European-Finnish (FIN)

AF:

0.101

AC:

1073

AN:

10610

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.149

AC:

10133

AN:

67996

Other (OTH)

AF:

0.178

AC:

376

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

811

1622

2434

3245

4056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.137

Hom.:

240

Bravo

AF:

0.136

Asia WGS

AF:

0.287

AC:

997

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.5

(source)

DANN

Benign

0.34

PhyloP100

0.15

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over