X-56785262-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -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

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 Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NBDY	NM_001348129.2	c.*167-32058C>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.*167-32058C>T		intron_variant	Intron 2 of 2	1	NM_001348129.2	ENSP00000489583.1
NBDY	ENST00000423617.2	c.*30-32058C>T		intron_variant	Intron 1 of 1	2		ENSP00000489486.1
NBDY	ENST00000637096.1	c.*167-25758C>T		intron_variant	Intron 2 of 3	3		ENSP00000490217.1
NBDY	ENST00000451583.1	n.*127-32058C>T		intron_variant	Intron 2 of 2	5		ENSP00000489367.1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 77459 AN: 109686 Hom.: 19626 Cov.: 22 AF XY: 0.707 AC XY: 22621 AN XY: 31982

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

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.615

Alfa AF: 0.735 Hom.: 42002

Bravo AF: 0.684

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs4826508; hg19: chrX-56811695;