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GeneBe

2-127048046-AT-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_139343.3(BIN1):c.*479del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 150064 control chromosomes in the gnomAD Genomes database, including 107 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.027 ( 107 hom., cov: 33)

Consequence

BIN1
NM_139343.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.103

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0652 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BIN1NM_139343.3 linkuse as main transcriptc.*479del 3_prime_UTR_variant 19/19 ENST00000316724.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BIN1ENST00000316724.10 linkuse as main transcriptc.*479del 3_prime_UTR_variant 19/191 NM_139343.3 O00499-1

Frequencies

GnomAD3 genomes
AF:
0.0270
AC:
4052
AN:
150064
Hom.:
107
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0673
Gnomad AMI
AF:
0.00222
Gnomad AMR
AF:
0.0588
Gnomad ASJ
AF:
0.000291
Gnomad EAS
AF:
0.0195
Gnomad SAS
AF:
0.0235
Gnomad FIN
AF:
0.000492
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00208
Gnomad OTH
AF:
0.0223
GnomAD4 exome
AF:
0.0193
AC:
744
AN:
38624
Hom.:
5
AF XY:
0.0187
AC XY:
373
AN XY:
19954
show subpopulations
Gnomad4 AFR exome
AF:
0.0481
Gnomad4 AMR exome
AF:
0.0729
Gnomad4 ASJ exome
AF:
0.0127
Gnomad4 EAS exome
AF:
0.0275
Gnomad4 SAS exome
AF:
0.0216
Gnomad4 FIN exome
AF:
0.0110
Gnomad4 NFE exome
AF:
0.0110
Gnomad4 OTH exome
AF:
0.0180
Bravo
AF:
0.0333

ClinVar

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

Submissions by phenotype

Myopathy, centronuclear, 2 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

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: rs367627116; hg19: chr2-127805622; API