chrX-56785262-C-T

Variant names:

• chrX-56785262-C-T
• rs4826508
• NM_001348129.2:c.*167-32058C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001348129.2(NBDY):​c.*167-32058C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 (19620 hom., 22667 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: NBDY NM_001348129.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 11 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348129.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NBDY	NM_001348129.2	MANE Select	c.*167-32058C>T		intron	N/A	NP_001335058.1	A0A0U1RRE5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NBDY	ENST00000374922.9	TSL:1 MANE Select	c.*167-32058C>T		intron	N/A	ENSP00000489583.1	A0A0U1RRE5
	NBDY	ENST00000423617.2	TSL:2	c.*30-32058C>T		intron	N/A	ENSP00000489486.1	A0A0U1RRE5
	NBDY	ENST00000637096.1	TSL:3	c.*167-25758C>T		intron	N/A	ENSP00000490217.1	A0A0U1RRE5

Frequencies

GnomAD3 genomes AF: 0.706 AC: 77459 AN: 109686 Hom.: 19626 Cov.: 22

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.457

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.624

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.706 AC: 77489 AN: 109738 Hom.: 19620 Cov.: 22 AF XY: 0.707 AC XY: 22667 AN XY: 32044

African (AFR) AF: 0.642 AC: 19254 AN: 29988

American (AMR) AF: 0.619 AC: 6442 AN: 10403

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1446 AN: 2620

East Asian (EAS) AF: 0.668 AC: 2281 AN: 3416

South Asian (SAS) AF: 0.680 AC: 1723 AN: 2532

European-Finnish (FIN) AF: 0.828 AC: 4773 AN: 5764

Middle Eastern (MID) AF: 0.460 AC: 98 AN: 213

European-Non Finnish (NFE) AF: 0.759 AC: 39959 AN: 52629

Other (OTH) AF: 0.615 AC: 919 AN: 1495

Alfa AF: 0.722 Hom.: 61769

Bravo AF: 0.684

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.27
PhyloP100		-0.92

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: rs4826508; hg19: chrX-56811695;