NM_052951.3:c.795+475G>A

Variant names:

• chr20-45809660-G-A
• rs399672
• NM_052951.3:c.795+475G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052951.3(DNTTIP1):​c.795+475G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,116 control chromosomes in the GnomAD database, including 38,494 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 0.71 (38494 hom., cov: 33)
• Consequence: DNTTIP1 NM_052951.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 14 publications found

Genes affected

DNTTIP1 (HGNC:16160): (deoxynucleotidyltransferase terminal interacting protein 1) DNTTIP1 binds DNA and enhances the activity of terminal deoxynucleotidyltransferase (TDT, or DNTT; MIM 187410), a DNA polymerase that catalyzes the polymerization of DNA in the absence of a DNA template (Yamashita et al., 2001 [PubMed 11473582]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNTTIP1	NM_052951.3	c.795+475G>A		intron_variant	Intron 11 of 12	ENST00000372622.8	NP_443183.1
DNTTIP1	XM_024451823.2	c.675+475G>A		intron_variant	Intron 11 of 12		XP_024307591.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNTTIP1	ENST00000372622.8	c.795+475G>A		intron_variant	Intron 11 of 12	1	NM_052951.3	ENSP00000361705.3
DNTTIP1	ENST00000456939.5	c.645+475G>A		intron_variant	Intron 10 of 11	5		ENSP00000401024.1
DNTTIP1	ENST00000435014.1	c.502-1225G>A		intron_variant	Intron 8 of 9	5		ENSP00000400573.1

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107894 AN: 151996 Hom.: 38453 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.634

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.701

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.710 AC: 107999 AN: 152116 Hom.: 38494 Cov.: 33 AF XY: 0.706 AC XY: 52492 AN XY: 74356

African (AFR) AF: 0.709 AC: 29433 AN: 41488

American (AMR) AF: 0.767 AC: 11727 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3237 AN: 5170

South Asian (SAS) AF: 0.567 AC: 2738 AN: 4828

European-Finnish (FIN) AF: 0.696 AC: 7360 AN: 10568

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.720 AC: 48947 AN: 67984

Other (OTH) AF: 0.700 AC: 1478 AN: 2110

Alfa AF: 0.712 Hom.: 29880

Bravo AF: 0.719

Asia WGS AF: 0.657 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	5.4
DANN	Benign	0.85
PhyloP100		-1.5
Mutation Taster		=100/0	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: rs399672; hg19: chr20-44438299;