Variant chr11-108222481-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002519.3(NPAT):c.37+19T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 1,611,720 control chromosomes in the GnomAD database, including 257,342 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 22720 hom., cov: 32)

Exomes 𝑓: 0.56 ( 234622 hom. )

Consequence

NPAT
NM_002519.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.172

Variant links:

Genes affected

NPAT (HGNC:7896): (nuclear protein, coactivator of histone transcription) Enables protein C-terminus binding activity; transcription coactivator activity; and transcription corepressor activity. Involved in positive regulation of transcription by RNA polymerase II and regulation of transcription involved in G1/S transition of mitotic cell cycle. Located in Cajal body; Gemini of coiled bodies; and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

NPAT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 11-108222481-A-T is Benign according to our data. Variant chr11-108222481-A-T is described in ClinVar as [Benign]. Clinvar id is 2413966.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
NPAT	NM_002519.3 linkuse as main transcript	c.37+19T>A	intron_variant	ENST00000278612.9	NP_002510.2
NPAT	NM_001321307.1 linkuse as main transcript	c.37+19T>A	intron_variant		NP_001308236.1
NPAT	XM_011542854.3 linkuse as main transcript	c.37+19T>A	intron_variant		XP_011541156.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
NPAT	ENST00000278612.9 linkuse as main transcript	c.37+19T>A	intron_variant	1	NM_002519.3	ENSP00000278612	P1
NPAT	ENST00000531384.1 linkuse as main transcript	c.37+19T>A	intron_variant, NMD_transcript_variant	5		ENSP00000433497
NPAT	ENST00000610253.5 linkuse as main transcript	n.137+19T>A	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.540

AC:

82055

AN:

151902

Hom.:

22707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.423

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.629

Gnomad ASJ

AF:

0.642

Gnomad EAS

AF:

0.445

Gnomad SAS

AF:

0.648

Gnomad FIN

AF:

0.630

Gnomad MID

AF:

0.750

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.571

GnomAD3 exomes

AF:

0.579

AC:

142830

AN:

246702

Hom.:

41993

AF XY:

0.583

AC XY:

78097

AN XY:

133868

show subpopulations

Gnomad AFR exome

AF:

0.416

Gnomad AMR exome

AF:

0.654

Gnomad ASJ exome

AF:

0.618

Gnomad EAS exome

AF:

0.438

Gnomad SAS exome

AF:

0.642

Gnomad FIN exome

AF:

0.632

Gnomad NFE exome

AF:

0.569

Gnomad OTH exome

AF:

0.602

GnomAD4 exome

AF:

0.565

AC:

824564

AN:

1459700

Hom.:

234622

Cov.:

AF XY:

0.569

AC XY:

413100

AN XY:

725998

show subpopulations

Gnomad4 AFR exome

AF:

0.419

Gnomad4 AMR exome

AF:

0.649

Gnomad4 ASJ exome

AF:

0.615

Gnomad4 EAS exome

AF:

0.470

Gnomad4 SAS exome

AF:

0.643

Gnomad4 FIN exome

AF:

0.627

Gnomad4 NFE exome

AF:

0.558

Gnomad4 OTH exome

AF:

0.562

GnomAD4 genome

AF:

0.540

AC:

82096

AN:

152020

Hom.:

22720

Cov.:

AF XY:

0.548

AC XY:

40704

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.423

Gnomad4 AMR

AF:

0.628

Gnomad4 ASJ

AF:

0.642

Gnomad4 EAS

AF:

0.445

Gnomad4 SAS

AF:

0.650

Gnomad4 FIN

AF:

0.630

Gnomad4 NFE

AF:

0.569

Gnomad4 OTH

AF:

0.572

Alfa

AF:

0.564

Hom.:

4544

Bravo

AF:

0.532

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

7.8

DANN

Benign

0.65

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over