rs2235970

Variant names:

• chr1-93879581-G-A
• rs2235970
• ENST00000460191.1:n.338C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-93879581-G-A
• chr1-93879581-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460191.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DNTTIP2	ENST00000460191.1	TSL:2	n.338C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000310419	ENST00000849663.1		n.36+43G>A		intron	N/A
	ENSG00000310419	ENST00000849664.1		n.250+43G>A		intron	N/A

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

African (AFR) AF: 0.405 AC: 6471 AN: 15988

American (AMR) AF: 0.722 AC: 1305 AN: 1808

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 3272 AN: 5316

East Asian (EAS) AF: 0.729 AC: 2772 AN: 3802

South Asian (SAS) AF: 0.605 AC: 10534 AN: 17416

European-Finnish (FIN) AF: 0.534 AC: 222 AN: 416

Middle Eastern (MID) AF: 0.579 AC: 956 AN: 1652

European-Non Finnish (NFE) AF: 0.627 AC: 480163 AN: 765826

Other (OTH) AF: 0.621 AC: 17177 AN: 27656

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

African (AFR) AF: 0.427 AC: 17731 AN: 41504

American (AMR) AF: 0.711 AC: 10876 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2195 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3828 AN: 5180

South Asian (SAS) AF: 0.613 AC: 2957 AN: 4822

European-Finnish (FIN) AF: 0.543 AC: 5745 AN: 10572

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42405 AN: 67986

Other (OTH) AF: 0.599 AC: 1268 AN: 2116

Alfa AF: 0.617 Hom.: 51605

Bravo AF: 0.583

Asia WGS AF: 0.684 AC: 2376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-1.0
PromoterAI		0.0040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2235970; hg19: chr1-94345137;