rs7044

Positions:

• chrX-56817338-G-A

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.87

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=-0.96).
• 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	c.*185G>A		3_prime_UTR_variant	3/3	ENST00000374922.9	NP_001335058.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NBDY	ENST00000374922.9	c.*185G>A		3_prime_UTR_variant	3/3	1	NM_001348129.2	ENSP00000489583	P1
NBDY	ENST00000423617.2	c.*48G>A		3_prime_UTR_variant	2/2	2		ENSP00000489486	P1
NBDY	ENST00000637096.1	c.*345G>A		3_prime_UTR_variant	4/4	3		ENSP00000490217	P1
NBDY	ENST00000451583.1	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.: 23 AF XY: 0.579 AC XY: 18928 AN XY: 32666

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: 0 AN: 1 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.569 AC: 62907 AN: 110474 Hom.: 15545 Cov.: 23 AF XY: 0.578 AC XY: 18928 AN XY: 32728

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

Other links and lift over

dbSNP: rs7044; hg19: chrX-56843771;