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GeneBe

2-218660612-C-T

Variant summary

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

The NM_001079866.2(BCS1L):c.-49-327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151906 control chromosomes in the gnomAD Genomes database, including 19743 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.47 ( 19743 hom., cov: 32)

Consequence

BCS1L
NM_001079866.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.182

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=-0.85).
BP6
?
Variant 2-218660612-C-T is Benign according to our data. Variant chr2-218660612-C-T is described in ClinVar as [Benign]. Clinvar id is 669695.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BCS1LNM_001079866.2 linkuse as main transcriptc.-49-327C>T intron_variant ENST00000359273.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BCS1LENST00000359273.8 linkuse as main transcriptc.-49-327C>T intron_variant 1 NM_001079866.2 P1

Frequencies

GnomAD3 genomes
AF:
0.467
AC:
70944
AN:
151906
Hom.:
19743
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.148
Gnomad AMI
AF:
0.617
Gnomad AMR
AF:
0.553
Gnomad ASJ
AF:
0.600
Gnomad EAS
AF:
0.820
Gnomad SAS
AF:
0.675
Gnomad FIN
AF:
0.573
Gnomad MID
AF:
0.630
Gnomad NFE
AF:
0.573
Gnomad OTH
AF:
0.519
GnomAD4 exome
AF:
0.577
AC:
50003
AN:
86602
Hom.:
15325
AF XY:
0.587
AC XY:
26077
AN XY:
44388
show subpopulations
Gnomad4 AFR exome
AF:
0.127
Gnomad4 AMR exome
AF:
0.573
Gnomad4 ASJ exome
AF:
0.592
Gnomad4 EAS exome
AF:
0.827
Gnomad4 SAS exome
AF:
0.657
Gnomad4 FIN exome
AF:
0.566
Gnomad4 NFE exome
AF:
0.571
Gnomad4 OTH exome
AF:
0.566
Alfa
AF:
0.508
Hom.:
2655
Bravo
AF:
0.449
Asia WGS
AF:
0.699
AC:
2429
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 14, 2018This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
6.0
Dann
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.21
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.21
Position offset: 23

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: rs3770218; hg19: chr2-219525335; API