X-56781150-A-T

Position:

• chrX-56781150-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001348129.2(NBDY):​c.*167-36170A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 110,252 control chromosomes in the GnomAD database, including 14,218 homozygotes. There are 17,893 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 0.54 (14218 hom., 17893 hem., cov: 22)
• Consequence: NBDY NM_001348129.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NBDY	NM_001348129.2	c.*167-36170A>T		intron_variant		ENST00000374922.9	NP_001335058.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NBDY	ENST00000374922.9	c.*167-36170A>T		intron_variant		1	NM_001348129.2	ENSP00000489583.1
NBDY	ENST00000423617.2	c.*30-36170A>T		intron_variant		2		ENSP00000489486.1
NBDY	ENST00000637096.1	c.*167-29870A>T		intron_variant		3		ENSP00000490217.1
NBDY	ENST00000451583.1	n.*127-36170A>T		intron_variant		5		ENSP00000489367.1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 59543 AN: 110198 Hom.: 14226 Cov.: 22 AF XY: 0.551 AC XY: 17891 AN XY: 32466

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.540 AC: 59520 AN: 110252 Hom.: 14218 Cov.: 22 AF XY: 0.550 AC XY: 17893 AN XY: 32530

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.491

Alfa AF: 0.488 Hom.: 2550

Bravo AF: 0.498

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
DANN	Benign	0.070

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: rs5914796; hg19: chrX-56807583;