1-93879160-C-T

Variant names:

• chr1-93879160-C-T
• rs2235971
• NM_014597.5:c.-12G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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]

ENSG00000310419 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014597.5. 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
	DNTTIP2	NM_014597.5	MANE Select	c.-12G>A		5_prime_UTR	Exon 1 of 7	NP_055412.2	Q5QJE6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNTTIP2	ENST00000436063.7	TSL:1 MANE Select	c.-12G>A		5_prime_UTR	Exon 1 of 7	ENSP00000411010.2	Q5QJE6
	DNTTIP2	ENST00000528680.1	TSL:3	c.-12G>A		5_prime_UTR	Exon 1 of 2	ENSP00000434261.1	E9PRB3
	DNTTIP2	ENST00000359208.6	TSL:2	n.-12G>A		non_coding_transcript_exon	Exon 1 of 6	ENSP00000352137.6	J3KP30

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

GnomAD2 exomes AF: 0.361 AC: 88527 AN: 245134 AF XY: 0.367

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 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

African (AFR) AF: 0.135 AC: 4492 AN: 33380

American (AMR) AF: 0.387 AC: 17126 AN: 44252

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 8920 AN: 26042

East Asian (EAS) AF: 0.574 AC: 22653 AN: 39474

South Asian (SAS) AF: 0.463 AC: 39835 AN: 86124

European-Finnish (FIN) AF: 0.292 AC: 15209 AN: 52054

Middle Eastern (MID) AF: 0.377 AC: 2165 AN: 5748

European-Non Finnish (NFE) AF: 0.340 AC: 377664 AN: 1110808

Other (OTH) AF: 0.350 AC: 21081 AN: 60244

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

African (AFR) AF: 0.144 AC: 6003 AN: 41554

American (AMR) AF: 0.347 AC: 5312 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3472

East Asian (EAS) AF: 0.564 AC: 2909 AN: 5158

South Asian (SAS) AF: 0.479 AC: 2311 AN: 4822

European-Finnish (FIN) AF: 0.283 AC: 3000 AN: 10608

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 23001 AN: 67994

Other (OTH) AF: 0.321 AC: 677 AN: 2112

Alfa AF: 0.325 Hom.: 23240

Bravo AF: 0.292

Asia WGS AF: 0.499 AC: 1736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.3
DANN	Benign	0.84
PhyloP100		-0.043
PromoterAI		0.086	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Mutation Taster		=294/6	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

Other links and lift over

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