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GeneBe

2-218660859-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001079866.2(BCS1L):c.-49-80A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.99 in 152220 control chromosomes in the gnomAD Genomes database, including 74575 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.99 ( 74575 hom., cov: 32)

Consequence

BCS1L
NM_001079866.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.389

Links

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BP6
?
Variant 2-218660859-A-G is Benign according to our data. Variant chr2-218660859-A-G is described in ClinVar as [Benign]. Clinvar id is 1179749.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCS1LNM_001079866.2 linkuse as main transcriptc.-49-80A>G intron_variant ENST00000359273.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCS1LENST00000359273.8 linkuse as main transcriptc.-49-80A>G intron_variant 1 NM_001079866.2 P1

Frequencies

GnomAD3 genomes
AF:
0.990
AC:
150655
AN:
152220
Hom.:
74575
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.964
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.996
Gnomad ASJ
AF:
1.00
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
1.00
Gnomad FIN
AF:
1.00
Gnomad MID
AF:
1.00
Gnomad NFE
AF:
1.00
Gnomad OTH
AF:
0.995
GnomAD4 exome
AF:
0.999
AC:
869898
AN:
870998
Hom.:
434424
AF XY:
0.999
AC XY:
449136
AN XY:
449616
show subpopulations
Gnomad4 AFR exome
AF:
0.965
Gnomad4 AMR exome
AF:
0.998
Gnomad4 ASJ exome
AF:
1.00
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
1.00
Gnomad4 OTH exome
AF:
0.997
Alfa
AF:
0.993
Hom.:
10022
Bravo
AF:
0.989
Asia WGS
AF:
0.996
AC:
3462
AN:
3478

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 testingGeneDxJun 23, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
2.9
Dann
Benign
0.57
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs6722185; hg19: chr2-219525582; API