rs7044

Variant names:

• chrX-56817338-G-A
• rs7044
• NM_001348129.2:c.*185G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

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.*185G>A		3_prime_UTR	Exon 3 of 3	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.*185G>A		3_prime_UTR	Exon 3 of 3	ENSP00000489583.1	A0A0U1RRE5
	NBDY	ENST00000423617.2	TSL:2	c.*48G>A		3_prime_UTR	Exon 2 of 2	ENSP00000489486.1	A0A0U1RRE5
	NBDY	ENST00000637096.1	TSL:3	c.*345G>A		3_prime_UTR	Exon 4 of 4	ENSP00000490217.1	A0A0U1RRE5

Frequencies

GnomAD3 genomes AF: 0.570 AC: 62931 AN: 110420 Hom.: 15553 Cov.: 23

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.138 AC: 4229 AN: 30559

American (AMR) AF: 0.571 AC: 5865 AN: 10280

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1508 AN: 2629

East Asian (EAS) AF: 0.668 AC: 2341 AN: 3505

South Asian (SAS) AF: 0.626 AC: 1614 AN: 2578

European-Finnish (FIN) AF: 0.858 AC: 4984 AN: 5811

Middle Eastern (MID) AF: 0.413 AC: 88 AN: 213

European-Non Finnish (NFE) AF: 0.775 AC: 40870 AN: 52720

Other (OTH) AF: 0.517 AC: 776 AN: 1500

Alfa AF: 0.600 Hom.: 5528

Bravo AF: 0.528

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.70
PhyloP100		-2.9

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: rs7044; hg19: chrX-56843771;