Variant rs2241712 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_030578.4(B9D2):c.-5+107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 523,738 control chromosomes in the GnomAD database, including 118,895 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 38420 hom., cov: 34)

Exomes 𝑓: 0.65 ( 80475 hom. )

Consequence

B9D2
NM_030578.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.46

Variant links:

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]

B9D2 links:

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]

TMEM91 links:

ENSG00000255730 (HGNC:):

ENSG00000255730 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 19-41363851-C-T is Benign according to our data. Variant chr19-41363851-C-T is described in ClinVar as [Benign]. Clinvar id is 1167460.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
B9D2	NM_030578.4 link	c.-5+107G>A	intron_variant		ENST00000243578.8	NP_085055.2	Q9BPU9
B9D2	XM_011527349.3 link	c.-92G>A	5_prime_UTR_variant	1/4		XP_011525651.1	Q9BPU9
B9D2	XM_011527350.3 link	c.-72+107G>A	intron_variant			XP_011525652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B9D2	ENST00000243578.8 link	c.-5+107G>A		intron_variant		1	NM_030578.4	ENSP00000243578.2		Q9BPU9

Frequencies

GnomAD3 genomes

AF:

0.703

AC:

106845

AN:

152064

Hom.:

38383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.832

Gnomad AMI

AF:

0.816

Gnomad AMR

AF:

0.581

Gnomad ASJ

AF:

0.538

Gnomad EAS

AF:

0.442

Gnomad SAS

AF:

0.614

Gnomad FIN

AF:

0.716

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.684

Gnomad OTH

AF:

0.652

GnomAD4 exome

AF:

0.652

AC:

242384

AN:

371554

Hom.:

80475

AF XY:

0.647

AC XY:

127464

AN XY:

197034

show subpopulations

Gnomad4 AFR exome

AF:

0.827

Gnomad4 AMR exome

AF:

0.541

Gnomad4 ASJ exome

AF:

0.526

Gnomad4 EAS exome

AF:

0.474

Gnomad4 SAS exome

AF:

0.608

Gnomad4 FIN exome

AF:

0.722

Gnomad4 NFE exome

AF:

0.679

Gnomad4 OTH exome

AF:

0.645

GnomAD4 genome

AF:

0.703

AC:

106943

AN:

152184

Hom.:

38420

Cov.:

AF XY:

0.697

AC XY:

51852

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.832

Gnomad4 AMR

AF:

0.580

Gnomad4 ASJ

AF:

0.538

Gnomad4 EAS

AF:

0.443

Gnomad4 SAS

AF:

0.614

Gnomad4 FIN

AF:

0.716

Gnomad4 NFE

AF:

0.684

Gnomad4 OTH

AF:

0.650

Alfa

AF:

0.702

Hom.:

8125

Bravo

AF:

0.698

Asia WGS

AF:

0.551

AC:

1912

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.089

DANN

Benign

0.80

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over