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GeneBe

2-218660306-G-A

Variant summary

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

The NM_001079866.2(BCS1L):c.-50+563G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0258 in 152178 control chromosomes in the gnomAD Genomes database, including 162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.026 ( 162 hom., cov: 32)

Consequence

BCS1L
NM_001079866.2 intron

Scores

2
Splicing: ADA: 0.00003753
2

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.357

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=-0.8).
BP6
?
Variant 2-218660306-G-A is Benign according to our data. Variant chr2-218660306-G-A is described in ClinVar as [Benign]. Clinvar id is 1259989. Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCS1LNM_001079866.2 linkuse as main transcriptc.-50+563G>A intron_variant ENST00000359273.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCS1LENST00000359273.8 linkuse as main transcriptc.-50+563G>A intron_variant 1 NM_001079866.2 P1

Frequencies

GnomAD3 genomes
AF:
0.0258
AC:
3930
AN:
152178
Hom.:
162
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0905
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00746
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.000250
Gnomad OTH
AF:
0.0230
Alfa
AF:
0.0218
Hom.:
8
Bravo
AF:
0.0293
Asia WGS
AF:
0.00491
AC:
17
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

GRACILE syndrome Benign:1
Benign, no assertion criteria providedclinical testingNatera, Inc.Nov 11, 2019- -
not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 09, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
12
Dann
Benign
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000038
dbscSNV1_RF
Benign
0.012
SpliceAI score (max)
0.070
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: rs77595651; hg19: chr2-219525029; API