chr1-23557842-C-G

Variant names:

• chr1-23557842-C-G
• rs2071495
• ENST00000826972.1:n.204-14905C>G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 5 publications found

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826972.1. 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.*599G>C		downstream_gene	N/A	NP_002158.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307540	ENST00000826972.1		n.204-14905C>G		intron	N/A
	ID3	ENST00000374561.6	TSL:1 MANE Select	c.*599G>C		downstream_gene	N/A	ENSP00000363689.5	Q02535
	ID3	ENST00000856197.1		c.*592G>C		downstream_gene	N/A	ENSP00000526256.1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19839 AN: 152136 Hom.: 2112 Cov.: 32

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: 56 AN: 450 Hom.: 5 AF XY: 0.112 AC XY: 31 AN XY: 276

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.114 AC: 48 AN: 422

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.313 AC: 5 AN: 16

Other (OTH) AF: 0.250 AC: 3 AN: 12

GnomAD4 genome AF: 0.130 AC: 19825 AN: 152254 Hom.: 2107 Cov.: 32 AF XY: 0.131 AC XY: 9715 AN XY: 74432

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: 55 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10133 AN: 67996

Other (OTH) AF: 0.178 AC: 376 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.5
DANN	Benign	0.34
PhyloP100		0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2071495; hg19: chr1-23884333;