1-93879160-C-T

Position:

• chr1-93879160-C-T

Variant summary

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

The NM_014597.5(DNTTIP2):​c.-12G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 1,610,352 control chromosomes in the GnomAD database, including 99,809 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 0.30 (7566 hom., cov: 34)
  • Exomes 𝑓: 0.35 (92243 hom.)
• Consequence: DNTTIP2 NM_014597.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

DNTTIP2 (HGNC:24013): (deoxynucleotidyltransferase terminal interacting protein 2) This gene is thought to be involved in chromatin remodeling and gene transcription. The encoded nuclear protein binds to and enhances the transcriptional activity of the estrogen receptor alpha, and also interacts with terminal deoxynucleotidyltransferase. The expression profile of this gene is a potential biomarker for chronic obstructive pulmonary disease. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNTTIP2	NM_014597.5	c.-12G>A		5_prime_UTR_variant	1/7	ENST00000436063.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNTTIP2	ENST00000436063.7	c.-12G>A		5_prime_UTR_variant	1/7	1	NM_014597.5	P1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44923 AN: 152108 Hom.: 7564 Cov.: 34

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.322

GnomAD3 exomes AF: 0.361 AC: 88527 AN: 245134 Hom.: 17176 AF XY: 0.367 AC XY: 48887 AN XY: 133266

Gnomad AFR exome AF: 0.135

Gnomad AMR exome AF: 0.392

Gnomad ASJ exome AF: 0.346

Gnomad EAS exome AF: 0.564

Gnomad SAS exome AF: 0.466

Gnomad FIN exome AF: 0.288

Gnomad NFE exome AF: 0.337

Gnomad OTH exome AF: 0.356

GnomAD4 exome AF: 0.349 AC: 509145 AN: 1458126 Hom.: 92243 Cov.: 51 AF XY: 0.353 AC XY: 256368 AN XY: 725434

Gnomad4 AFR exome AF: 0.135

Gnomad4 AMR exome AF: 0.387

Gnomad4 ASJ exome AF: 0.343

Gnomad4 EAS exome AF: 0.574

Gnomad4 SAS exome AF: 0.463

Gnomad4 FIN exome AF: 0.292

Gnomad4 NFE exome AF: 0.340

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.295 AC: 44934 AN: 152226 Hom.: 7566 Cov.: 34 AF XY: 0.298 AC XY: 22153 AN XY: 74432

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.321

Alfa AF: 0.337 Hom.: 15518

Bravo AF: 0.292

Asia WGS AF: 0.499 AC: 1736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.3
DANN	Benign	0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs2235971; hg19: chr1-94344716; COSMIC: COSV63283940; COSMIC: COSV63283940;