rs2235970

chr1-93879581-G-Achr1-93879581-G-C

Variant summary

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

The ENST00000460191.1(DNTTIP2):n.338C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 992,030 control chromosomes in the GnomAD database, including 189,553 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 0.58 (26112 hom., cov: 33)
  • Exomes 𝑓: 0.62 (163441 hom.)
• Consequence: DNTTIP2 ENST00000460191.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNTTIP2	ENST00000460191.1	n.338C>T		non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87717 AN: 152030 Hom.: 26103 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.599

GnomAD4 exome AF: 0.623 AC: 522872 AN: 839880 Hom.: 163441 Cov.: 35 AF XY: 0.623 AC XY: 241841 AN XY: 388274

Gnomad4 AFR exome AF: 0.405

Gnomad4 AMR exome AF: 0.722

Gnomad4 ASJ exome AF: 0.616

Gnomad4 EAS exome AF: 0.729

Gnomad4 SAS exome AF: 0.605

Gnomad4 FIN exome AF: 0.534

Gnomad4 NFE exome AF: 0.627

Gnomad4 OTH exome AF: 0.621

GnomAD4 genome AF: 0.577 AC: 87767 AN: 152150 Hom.: 26112 Cov.: 33 AF XY: 0.579 AC XY: 43044 AN XY: 74380

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.599

Alfa AF: 0.620 Hom.: 38692

Bravo AF: 0.583

Asia WGS AF: 0.684 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.3
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2235970; hg19: chr1-94345137;