19-41355432-CCCT-CCCTCCT

Variant names:

• chr19-41355432-C-CCCT
• rs11466313
• NM_030578.4:c.215-422_215-420dupAGG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_030578.4(B9D2):​c.215-422_215-420dupAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.70 (37322 hom., cov: 0)
• Consequence: B9D2 NM_030578.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 10 publications found

Genes affected

B9D2 (HGNC:28636): (B9 domain containing 2) This gene encodes a B9 domain protein, which are exclusively found in ciliated organisms. The gene is upregulated during mucociliary differentiation, and the encoded protein localizes to basal bodies and cilia. Disrupting expression of this gene results in ciliogenesis defects. [provided by RefSeq, Oct 2009]

TMEM91 (HGNC:32393): (transmembrane protein 91) Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle and membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255730 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030578.4. 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
	B9D2	NM_030578.4	MANE Select	c.215-422_215-420dupAGG		intron	N/A	NP_085055.2	Q9BPU9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	B9D2	ENST00000243578.8	TSL:1 MANE Select	c.215-420_215-419insAGG		intron	N/A	ENSP00000243578.2	Q9BPU9
	TMEM91	ENST00000539627.5	TSL:1	c.-30+4230_-30+4231insCCT		intron	N/A	ENSP00000441900.1	F5GWC9
	TMEM91	ENST00000604123.5	TSL:3	c.142+1117_142+1118insCCT		intron	N/A	ENSP00000474871.1	S4R3Y8

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105380 AN: 151624 Hom.: 37285 Cov.: 0

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.695 AC: 105478 AN: 151744 Hom.: 37322 Cov.: 0 AF XY: 0.690 AC XY: 51194 AN XY: 74142

African (AFR) AF: 0.793 AC: 32808 AN: 41394

American (AMR) AF: 0.573 AC: 8739 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2281 AN: 5150

South Asian (SAS) AF: 0.622 AC: 2990 AN: 4806

European-Finnish (FIN) AF: 0.742 AC: 7801 AN: 10512

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46682 AN: 67848

Other (OTH) AF: 0.651 AC: 1370 AN: 2106

Alfa AF: 0.582 Hom.: 1520

Bravo AF: 0.685

Asia WGS AF: 0.548 AC: 1902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11466313; hg19: chr19-41861337;