X-56781150-A-T

Variant names:

• chrX-56781150-A-T
• rs5914796
• NM_001348129.2:c.*167-36170A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NBDY	NM_001348129.2	c.*167-36170A>T		intron_variant	Intron 2 of 2	ENST00000374922.9	NP_001335058.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.540 AC: 59543 AN: 110198 Hom.: 14226 Cov.: 22

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

African (AFR) AF: 0.110 AC: 3333 AN: 30396

American (AMR) AF: 0.549 AC: 5715 AN: 10401

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1403 AN: 2628

East Asian (EAS) AF: 0.671 AC: 2322 AN: 3459

South Asian (SAS) AF: 0.636 AC: 1615 AN: 2539

European-Finnish (FIN) AF: 0.824 AC: 4735 AN: 5749

Middle Eastern (MID) AF: 0.373 AC: 79 AN: 212

European-Non Finnish (NFE) AF: 0.740 AC: 38986 AN: 52684

Other (OTH) AF: 0.491 AC: 740 AN: 1508

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
PhyloP100		0.45

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: rs5914796; hg19: chrX-56807583;