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GeneBe

rs1800469

chr19-41354391-A-G

Variant summary

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

The ENST00000539627.5(TMEM91):c.-30+3189A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151848 control chromosomes in the gnomAD Genomes database, including 36420 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 36420 hom., cov: 31)

Consequence

TMEM91
ENST00000539627.5 intron

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -1.81

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 19-41354391-A-G is Benign according to our data. Variant chr19-41354391-A-G is described in ClinVar as [Benign]. Clinvar id is 39302. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
B9D2NM_030578.4 linkuse as main transcript downstream_gene_variant ENST00000243578.8
B9D2XM_011527349.3 linkuse as main transcript downstream_gene_variant
B9D2XM_011527350.3 linkuse as main transcript downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TMEM91ENST00000539627.5 linkuse as main transcriptc.-30+3189A>G intron_variant 1
TMEM91ENST00000604123.5 linkuse as main transcriptc.142+76A>G intron_variant 3
B9D2ENST00000243578.8 linkuse as main transcript downstream_gene_variant 1 NM_030578.4 P1
B9D2ENST00000675972.1 linkuse as main transcript downstream_gene_variant P1

Frequencies

GnomAD3 genomes
AF:
0.687
AC:
104346
AN:
151848
Hom.:
36420
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.763
Gnomad AMI
AF:
0.816
Gnomad AMR
AF:
0.571
Gnomad ASJ
AF:
0.545
Gnomad EAS
AF:
0.445
Gnomad SAS
AF:
0.621
Gnomad FIN
AF:
0.744
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.688
Gnomad OTH
AF:
0.644
GnomAD4 exome
AF:
0.659
AC:
288820
AN:
438204
Hom.:
96677
AF XY:
0.655
AC XY:
150231
AN XY:
229484
show subpopulations
Gnomad4 AFR exome
AF:
0.758
Gnomad4 AMR exome
AF:
0.545
Gnomad4 ASJ exome
AF:
0.534
Gnomad4 EAS exome
AF:
0.486
Gnomad4 SAS exome
AF:
0.619
Gnomad4 FIN exome
AF:
0.754
Gnomad4 NFE exome
AF:
0.687
Gnomad4 OTH exome
AF:
0.650
Alfa
AF:
0.673
Hom.:
62689
Bravo
AF:
0.677
Asia WGS
AF:
0.548
AC:
1904
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 submitterclinical testingInvitaeNov 01, 2022- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 30, 2020This variant is associated with the following publications: (PMID: 23703862, 15175276, 21761116, 22282866, 16207846, 21679448, 18670143, 19536820, 16896927, 17333284, 9887336, 19614955, 18547814, 20232138, 14597484, 19096005) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
Cadd
Benign
2.0
Dann
Benign
0.48

Splicing

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.

Other links and lift over

dbSNP: rs1800469; hg19: chr19-41860296;