19-41355432-CCCT-CCCTCCT

Position:

• chr19-41355432-CCCT-CCCTCCT

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B9D2	NM_030578.4	c.215-422_215-420dupAGG		intron_variant		ENST00000243578.8	NP_085055.2
B9D2	XM_011527349.3	c.215-422_215-420dupAGG		intron_variant			XP_011525651.1
B9D2	XM_011527350.3	c.56-422_56-420dupAGG		intron_variant			XP_011525652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B9D2	ENST00000243578.8	c.215-422_215-420dupAGG		intron_variant		1	NM_030578.4	ENSP00000243578.2

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

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.651

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 v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11466313; hg19: chr19-41861337;