rs1047014

Positions:

• chr6-19841262-T-C

Variant summary

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

The NM_001546.4(ID4):​c.*2067T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,186 control chromosomes in the GnomAD database, including 3,978 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 0.22 (3978 hom., cov: 33)
• Consequence: ID4 NM_001546.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

Genes affected

ID4 (HGNC:5363): (inhibitor of DNA binding 4) This gene encodes a member of the inhibitor of DNA binding (ID) protein family. The encoded protein lacks DNA binding ability, and instead regulates gene expression through binding to and inhibiting basic helix-loop-helix transcription factors. This protein has been implicated in the regulation of diverse cellular processes that play a role in development and tumorigenesis. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ID4	NM_001546.4	c.*2067T>C		3_prime_UTR_variant	3/3	ENST00000378700.8	NP_001537.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ID4	ENST00000378700.8	c.*2067T>C		3_prime_UTR_variant	3/3	1	NM_001546.4	ENSP00000367972.3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33721 AN: 152070 Hom.: 3980 Cov.: 33

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.217

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.222 AC: 33730 AN: 152186 Hom.: 3978 Cov.: 33 AF XY: 0.217 AC XY: 16149 AN XY: 74394

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.215

Alfa AF: 0.238 Hom.: 5517

Bravo AF: 0.218

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	18
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1047014; hg19: chr6-19841493;