20-50876068-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2

The NM_017843.4(BCAS4):​c.561C>T​(p.Ser187Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00068 in 454,578 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S187S) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.00046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00079 ( 3 hom. )

Consequence

BCAS4
NM_017843.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06
Variant links:
Genes affected
BCAS4 (HGNC:14367): (breast carcinoma amplified sequence 4) Predicted to be part of BLOC-1 complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP7
Synonymous conserved (PhyloP=-1.06 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BCAS4NM_198799.4 linkc.400-418C>T intron_variant Intron 4 of 4 ENST00000371608.8 NP_942094.3 Q8TDM0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BCAS4ENST00000371608.8 linkc.400-418C>T intron_variant Intron 4 of 4 1 NM_198799.4 ENSP00000360669.3 A0A804CEY2

Frequencies

GnomAD3 genomes
AF:
0.000460
AC:
70
AN:
152138
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.0115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000221
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.00115
AC:
146
AN:
127166
Hom.:
2
AF XY:
0.00121
AC XY:
84
AN XY:
69622
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000248
Gnomad ASJ exome
AF:
0.0137
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000181
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000445
Gnomad OTH exome
AF:
0.00126
GnomAD4 exome
AF:
0.000790
AC:
239
AN:
302440
Hom.:
3
Cov.:
0
AF XY:
0.000784
AC XY:
135
AN XY:
172258
show subpopulations
Gnomad4 AFR exome
AF:
0.000117
Gnomad4 AMR exome
AF:
0.000294
Gnomad4 ASJ exome
AF:
0.0143
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000151
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000290
Gnomad4 OTH exome
AF:
0.00120
GnomAD4 genome
AF:
0.000460
AC:
70
AN:
152138
Hom.:
0
Cov.:
32
AF XY:
0.000431
AC XY:
32
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000720
Gnomad4 ASJ
AF:
0.0115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000221
Gnomad4 OTH
AF:
0.000956
Alfa
AF:
0.00169
Hom.:
0
Bravo
AF:
0.000578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
1.8
DANN
Benign
0.66

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: rs762515527; hg19: chr20-49492605; API