rs1800468

Variant names:

Variant summary

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

The NM_030578.4(B9D2):c.*18G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0753 in 1,613,668 control chromosomes in the GnomAD database, including 5,061 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.059 ( 319 hom., cov: 32)

Exomes 𝑓: 0.077 ( 4742 hom. )

Consequence

B9D2
NM_030578.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.133

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 19-41354682-C-T is Benign according to our data. Variant chr19-41354682-C-T is described in ClinVar as [Benign]. Clinvar id is 261879.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-41354682-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
B9D2	NM_030578.4 link	c.*18G>A	3_prime_UTR_variant	Exon 4 of 4	ENST00000243578.8	NP_085055.2	Q9BPU9
B9D2	XM_011527349.3 link	c.*18G>A	3_prime_UTR_variant	Exon 4 of 4		XP_011525651.1	Q9BPU9
B9D2	XM_011527350.3 link	c.*18G>A	3_prime_UTR_variant	Exon 3 of 3		XP_011525652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
B9D2	ENST00000243578 link	c.*18G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_030578.4	ENSP00000243578.2		Q9BPU9

Frequencies

GnomAD3 genomes

AF:

0.0592

AC:

8998

AN:

152088

Hom.:

319

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0283

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.0633

Gnomad ASJ

AF:

0.0723

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0637

Gnomad FIN

AF:

0.0489

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0810

Gnomad OTH

AF:

0.0560

GnomAD3 exomes

AF:

0.0622

AC:

15532

AN:

249712

Hom.:

567

AF XY:

0.0642

AC XY:

8681

AN XY:

135236

show subpopulations

Gnomad AFR exome

AF:

0.0289

Gnomad AMR exome

AF:

0.0407

Gnomad ASJ exome

AF:

0.0731

Gnomad EAS exome

AF:

0.000436

Gnomad SAS exome

AF:

0.0682

Gnomad FIN exome

AF:

0.0527

Gnomad NFE exome

AF:

0.0827

Gnomad OTH exome

AF:

0.0648

GnomAD4 exome

AF:

0.0770

AC:

112467

AN:

1461462

Hom.:

4742

Cov.:

AF XY:

0.0772

AC XY:

56119

AN XY:

727032

show subpopulations

Gnomad4 AFR exome

AF:

0.0278

Gnomad4 AMR exome

AF:

0.0422

Gnomad4 ASJ exome

AF:

0.0712

Gnomad4 EAS exome

AF:

0.000353

Gnomad4 SAS exome

AF:

0.0676

Gnomad4 FIN exome

AF:

0.0517

Gnomad4 NFE exome

AF:

0.0846

Gnomad4 OTH exome

AF:

0.0753

GnomAD4 genome

AF:

0.0591

AC:

9000

AN:

152206

Hom.:

319

Cov.:

AF XY:

0.0578

AC XY:

4303

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0283

Gnomad4 AMR

AF:

0.0631

Gnomad4 ASJ

AF:

0.0723

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0637

Gnomad4 FIN

AF:

0.0489

Gnomad4 NFE

AF:

0.0810

Gnomad4 OTH

AF:

0.0554

Alfa

AF:

0.0737

Hom.:

140

Bravo

AF:

0.0588

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 9887336) -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

Benign:1

Dec 02, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Meckel syndrome, type 10

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.7

DANN

Benign

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.2

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