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GeneBe

14-23320430-A-AG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001387343.1(BCL2L2-PABPN1):c.528+605dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0476 in 152,276 control chromosomes in the GnomAD database, including 255 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.048 ( 255 hom., cov: 32)

Consequence

BCL2L2-PABPN1
NM_001387343.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.410
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 14-23320430-A-AG is Benign according to our data. Variant chr14-23320430-A-AG is described in ClinVar as [Benign]. Clinvar id is 1262184.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0729 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCL2L2-PABPN1NM_001387343.1 linkuse as main transcriptc.528+605dup intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0476
AC:
7246
AN:
152158
Hom.:
255
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0105
Gnomad AMI
AF:
0.0450
Gnomad AMR
AF:
0.0764
Gnomad ASJ
AF:
0.0646
Gnomad EAS
AF:
0.000384
Gnomad SAS
AF:
0.0454
Gnomad FIN
AF:
0.0431
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0674
Gnomad OTH
AF:
0.0435
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0476
AC:
7251
AN:
152276
Hom.:
255
Cov.:
32
AF XY:
0.0468
AC XY:
3486
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0105
Gnomad4 AMR
AF:
0.0765
Gnomad4 ASJ
AF:
0.0646
Gnomad4 EAS
AF:
0.000385
Gnomad4 SAS
AF:
0.0458
Gnomad4 FIN
AF:
0.0431
Gnomad4 NFE
AF:
0.0674
Gnomad4 OTH
AF:
0.0430
Alfa
AF:
0.0606
Hom.:
39
Bravo
AF:
0.0451

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxApr 12, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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.

Other links and lift over

dbSNP: rs147639247; hg19: chr14-23789639; API