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GeneBe

rs1799732

chr11-113475529-T-TG

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The XR_948024.2(LOC105369501):n.912_913insC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.80 ( 48687 hom., cov: 0)

Consequence

LOC105369501
XR_948024.2 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 1.45

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6
?
Variant 11-113475529-T-TG is Benign according to our data. Variant chr11-113475529-T-TG is described in ClinVar as [Benign]. Clinvar id is 1236510. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105369501XR_948024.2 linkuse as main transcriptn.912_913insC non_coding_transcript_exon_variant 6/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DRD2ENST00000540600.5 linkuse as main transcriptn.34+128_34+129insC intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.801
AC:
117209
AN:
146376
Hom.:
48687
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.524
Gnomad AMI
AF:
0.846
Gnomad AMR
AF:
0.860
Gnomad ASJ
AF:
0.940
Gnomad EAS
AF:
0.876
Gnomad SAS
AF:
0.891
Gnomad FIN
AF:
0.946
Gnomad MID
AF:
0.935
Gnomad NFE
AF:
0.903
Gnomad OTH
AF:
0.843
GnomAD4 exome
AF:
0.808
AC:
21
AN:
26
Hom.:
8
AF XY:
0.850
AC XY:
17
AN XY:
20
show subpopulations
Gnomad4 EAS exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.792
Alfa
AF:
0.808
Hom.:
8668
Bravo
AF:
0.765
Asia WGS
AF:
0.825
AC:
2841
AN:
3442

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJun 14, 2018- -
Dystonic disorder Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeOct 30, 2022- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs1799732; hg19: chr11-113346251;