rs399672

chr20-45809660-G-Achr20-45809660-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
DNTTIP1	NM_052951.3	c.795+475G>A		intron_variant		ENST00000372622.8
DNTTIP1	XM_024451823.2	c.675+475G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNTTIP1	ENST00000372622.8	c.795+475G>A		intron_variant		1	NM_052951.3	P1
DNTTIP1	ENST00000435014.1	c.504-1225G>A		intron_variant		5
DNTTIP1	ENST00000456939.5	c.646+475G>A		intron_variant		5

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

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.567

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.700

Alfa AF: 0.709 Hom.: 22182

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

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: rs399672; hg19: chr20-44438299;