rs2920

Positions:

• chr1-23558289-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ID3	NM_002167.5	c.*152A>G		3_prime_UTR_variant	3/3	ENST00000374561.6	NP_002158.3
LOC124903876	XR_007065537.1	n.282+6194T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ID3	ENST00000374561.6	c.*152A>G		3_prime_UTR_variant	3/3	1	NM_002167.5	ENSP00000363689.5
ID3	ENST00000463312.1	n.268A>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30244 AN: 152010 Hom.: 3084 Cov.: 32

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: 43 AN: 334 Hom.: 3 Cov.: 0 AF XY: 0.125 AC XY: 25 AN XY: 200

Gnomad4 AMR exome AF: 0.00

Gnomad4 SAS exome AF: 0.0833

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.137

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.199 AC: 30291 AN: 152128 Hom.: 3091 Cov.: 32 AF XY: 0.194 AC XY: 14458 AN XY: 74380

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.0872

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.191

Alfa AF: 0.201 Hom.: 4998

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	16
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

dbSNP: rs2920; hg19: chr1-23884780;