6-19841262-T-C

Variant names:

• chr6-19841262-T-C
• rs1047014
• NM_001546.4:c.*2067T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001546.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ID4	NM_001546.4	MANE Select	c.*2067T>C		3_prime_UTR	Exon 3 of 3	NP_001537.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ID4	ENST00000378700.8	TSL:1 MANE Select	c.*2067T>C		3_prime_UTR	Exon 3 of 3	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

African (AFR) AF: 0.229 AC: 9519 AN: 41522

American (AMR) AF: 0.199 AC: 3036 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5190

South Asian (SAS) AF: 0.112 AC: 540 AN: 4832

European-Finnish (FIN) AF: 0.215 AC: 2268 AN: 10570

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17132 AN: 67986

Other (OTH) AF: 0.215 AC: 454 AN: 2116

Alfa AF: 0.238 Hom.: 14166

Bravo AF: 0.218

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	18
DANN	Benign	0.81
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs1047014; hg19: chr6-19841493;