NM_022129.4:c.84+2009T>C

Variant names:

• chr10-68304752-A-G
• rs10733843
• NM_022129.4:c.84+2009T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022129.4(PBLD):​c.84+2009T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,162 control chromosomes in the GnomAD database, including 47,813 homozygotes. 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 0.79 (47813 hom., cov: 33)
• Consequence: PBLD NM_022129.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 1 publications found

Genes affected

PBLD (HGNC:23301): (phenazine biosynthesis like protein domain containing) Enables identical protein binding activity. Involved in maintenance of gastrointestinal epithelium; negative regulation of SMAD protein signal transduction; and negative regulation of transforming growth factor beta receptor signaling pathway. Located in cytoplasm. [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 = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022129.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBLD	NM_022129.4	MANE Select	c.84+2009T>C		intron	N/A	NP_071412.2
	PBLD	NM_001033083.2		c.84+2009T>C		intron	N/A	NP_001028255.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBLD	ENST00000358769.7	TSL:5 MANE Select	c.84+2009T>C		intron	N/A	ENSP00000351619.2
	PBLD	ENST00000309049.8	TSL:1	c.84+2009T>C		intron	N/A	ENSP00000308466.4
	PBLD	ENST00000495025.2	TSL:5	c.84+2009T>C		intron	N/A	ENSP00000476306.1

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119726 AN: 152044 Hom.: 47781 Cov.: 33

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.787 AC: 119814 AN: 152162 Hom.: 47813 Cov.: 33 AF XY: 0.783 AC XY: 58278 AN XY: 74392

African (AFR) AF: 0.668 AC: 27708 AN: 41474

American (AMR) AF: 0.776 AC: 11857 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3470

East Asian (EAS) AF: 0.847 AC: 4390 AN: 5184

South Asian (SAS) AF: 0.748 AC: 3607 AN: 4824

European-Finnish (FIN) AF: 0.790 AC: 8377 AN: 10602

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58369 AN: 68020

Other (OTH) AF: 0.806 AC: 1702 AN: 2112

Alfa AF: 0.832 Hom.: 26793

Bravo AF: 0.780

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.63
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

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: rs10733843; hg19: chr10-70064509;