rs2742946

Variant names:

• chr1-23559582-T-C
• rs2742946
• ENST00000826972.1:n.204-13165T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000826972.1(ENSG00000307540):​n.204-13165T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 913,402 control chromosomes in the GnomAD database, including 91,309 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 0.43 (14515 hom., cov: 34)
  • Exomes 𝑓: 0.44 (76794 hom.)
• Consequence: ENSG00000307540 ENST00000826972.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548

Genes affected

ENSG00000307540 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903876	XR_007065537.1	n.282+7487T>C		intron_variant	Intron 2 of 2
ID3	NM_002167.5	c.-156A>G		upstream_gene_variant		ENST00000374561.6	NP_002158.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307540	ENST00000826972.1	n.204-13165T>C		intron_variant	Intron 2 of 2
ID3	ENST00000374561.6	c.-156A>G		upstream_gene_variant		1	NM_002167.5	ENSP00000363689.5
ID3	ENST00000486541.1	n.-139A>G		upstream_gene_variant		1

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65741 AN: 152126 Hom.: 14523 Cov.: 34

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.468

GnomAD4 exome AF: 0.444 AC: 338106 AN: 761158 Hom.: 76794 Cov.: 10 AF XY: 0.443 AC XY: 169198 AN XY: 382214

African (AFR) AF: 0.360 AC: 6610 AN: 18368

American (AMR) AF: 0.396 AC: 7205 AN: 18174

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 7983 AN: 15462

East Asian (EAS) AF: 0.574 AC: 18353 AN: 31960

South Asian (SAS) AF: 0.361 AC: 18310 AN: 50770

European-Finnish (FIN) AF: 0.435 AC: 12839 AN: 29532

Middle Eastern (MID) AF: 0.497 AC: 1259 AN: 2532

European-Non Finnish (NFE) AF: 0.447 AC: 249534 AN: 558294

Other (OTH) AF: 0.444 AC: 16013 AN: 36066

GnomAD4 genome AF: 0.432 AC: 65748 AN: 152244 Hom.: 14515 Cov.: 34 AF XY: 0.430 AC XY: 32044 AN XY: 74460

African (AFR) AF: 0.370 AC: 15372 AN: 41556

American (AMR) AF: 0.414 AC: 6340 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2995 AN: 5172

South Asian (SAS) AF: 0.349 AC: 1687 AN: 4828

European-Finnish (FIN) AF: 0.437 AC: 4636 AN: 10610

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31292 AN: 67984

Other (OTH) AF: 0.467 AC: 986 AN: 2112

Alfa AF: 0.427 Hom.: 3676

Bravo AF: 0.433

Asia WGS AF: 0.426 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	18
DANN	Benign	0.41
PhyloP100		0.55
PromoterAI		0.024	Neutral
Mutation Taster		=300/0	polymorphism (auto)

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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Other links and lift over

dbSNP: rs2742946; hg19: chr1-23886073;