Variant X-56817338-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001348129.2(NBDY):c.*185G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 110,474 control chromosomes in the GnomAD database, including 15,545 homozygotes. There are 18,928 hemizygotes in GnomAD. 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 0.57 ( 15545 hom., 18928 hem., cov: 23)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

NBDY
NM_001348129.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.87

Variant links:

Genes affected

NBDY (HGNC:50713): (negative regulator of P-body association) Involved in negative regulation of cytoplasmic mRNA processing body assembly and nuclear-transcribed mRNA catabolic process. Located in P-body. [provided by Alliance of Genome Resources, Apr 2022]

NBDY links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBDY	NM_001348129.2 linkuse as main transcript	c.*185G>A		3_prime_UTR_variant	3/3	ENST00000374922.9	NP_001335058.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
NBDY	ENST00000374922.9 linkuse as main transcript	c.*185G>A	3_prime_UTR_variant	3/3	1	NM_001348129.2	ENSP00000489583	P1
NBDY	ENST00000423617.2 linkuse as main transcript	c.*48G>A	3_prime_UTR_variant	2/2	2		ENSP00000489486	P1
NBDY	ENST00000637096.1 linkuse as main transcript	c.*345G>A	3_prime_UTR_variant	4/4	3		ENSP00000490217	P1
NBDY	ENST00000451583.1 linkuse as main transcript	c.*145G>A	3_prime_UTR_variant, NMD_transcript_variant	3/3	5		ENSP00000489367

Frequencies

GnomAD3 genomes

AF:

0.570

AC:

62931

AN:

110420

Hom.:

15553

Cov.:

AF XY:

0.579

AC XY:

18928

AN XY:

32666

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.931

Gnomad AMR

AF:

0.571

Gnomad ASJ

AF:

0.574

Gnomad EAS

AF:

0.668

Gnomad SAS

AF:

0.627

Gnomad FIN

AF:

0.858

Gnomad MID

AF:

0.403

Gnomad NFE

AF:

0.775

Gnomad OTH

AF:

0.525

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.569

AC:

62907

AN:

110474

Hom.:

15545

Cov.:

AF XY:

0.578

AC XY:

18928

AN XY:

32728

show subpopulations

Gnomad4 AFR

AF:

0.138

Gnomad4 AMR

AF:

0.571

Gnomad4 ASJ

AF:

0.574

Gnomad4 EAS

AF:

0.668

Gnomad4 SAS

AF:

0.626

Gnomad4 FIN

AF:

0.858

Gnomad4 NFE

AF:

0.775

Gnomad4 OTH

AF:

0.517

Alfa

AF:

0.600

Hom.:

5528

Bravo

AF:

0.528

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.14

DANN

Benign

0.70

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over