NM_030578.4:c.89-1716C>T

Variant names:

• chr19-41359738-G-A
• rs11083616
• NM_030578.4:c.89-1716C>T

Variant summary

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

The NM_030578.4(B9D2):​c.89-1716C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,754 control chromosomes in the GnomAD database, including 27,459 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 0.60 (27459 hom., cov: 30)
• Consequence: B9D2 NM_030578.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 24 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
B9D2	NM_030578.4	c.89-1716C>T		intron_variant	Intron 2 of 3	ENST00000243578.8	NP_085055.2
B9D2	XM_011527349.3	c.89-1716C>T		intron_variant	Intron 2 of 3		XP_011525651.1
B9D2	XM_011527350.3	c.-71-1716C>T		intron_variant	Intron 1 of 2		XP_011525652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B9D2	ENST00000243578.8	c.89-1716C>T		intron_variant	Intron 2 of 3	1	NM_030578.4	ENSP00000243578.2

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90695 AN: 151638 Hom.: 27458 Cov.: 30

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.598 AC: 90728 AN: 151754 Hom.: 27459 Cov.: 30 AF XY: 0.598 AC XY: 44328 AN XY: 74132

African (AFR) AF: 0.606 AC: 25070 AN: 41364

American (AMR) AF: 0.522 AC: 7956 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1733 AN: 3472

East Asian (EAS) AF: 0.445 AC: 2286 AN: 5142

South Asian (SAS) AF: 0.547 AC: 2625 AN: 4800

European-Finnish (FIN) AF: 0.714 AC: 7525 AN: 10546

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41461 AN: 67874

Other (OTH) AF: 0.569 AC: 1201 AN: 2110

Alfa AF: 0.597 Hom.: 44323

Bravo AF: 0.584

Asia WGS AF: 0.507 AC: 1760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.28
PhyloP100		-0.076
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11083616; hg19: chr19-41865643;