rs1050096

Positions:

• chr1-23558170-G-A
• chr1-23558170-G-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855

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]

LOC124903876 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ID3	NM_002167.5	c.*271C>T		3_prime_UTR_variant	3/3	ENST00000374561.6	NP_002158.3
LOC124903876	XR_007065537.1	n.282+6075G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ID3	ENST00000374561.6	c.*271C>T		3_prime_UTR_variant	3/3	1	NM_002167.5	ENSP00000363689	P1
ID3	ENST00000463312.1	n.387C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99723 AN: 151880 Hom.: 33131 Cov.: 31

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.: 84 Cov.: 0 AF XY: 0.564 AC XY: 185 AN XY: 328

Gnomad4 AFR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.555

Gnomad4 NFE exome AF: 0.600

Gnomad4 OTH exome AF: 0.583

GnomAD4 genome AF: 0.657 AC: 99810 AN: 152000 Hom.: 33161 Cov.: 31 AF XY: 0.659 AC XY: 48956 AN XY: 74306

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.677

Alfa AF: 0.629 Hom.: 35939

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	13
DANN	Benign	0.86

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: rs1050096; hg19: chr1-23884661;