rs805301

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001387994.1(BAG6):​c.109-717T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,740 control chromosomes in the GnomAD database, including 15,637 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.

Frequency

Genomes: 𝑓 0.44 ( 15637 hom., cov: 30)

Consequence

BAG6
NM_001387994.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535
Variant links:
Genes affected
BAG6 (HGNC:13919): (BAG cochaperone 6) This gene was first characterized as part of a cluster of genes located within the human major histocompatibility complex class III region. This gene encodes a nuclear protein that is cleaved by caspase 3 and is implicated in the control of apoptosis. In addition, the protein forms a complex with E1A binding protein p300 and is required for the acetylation of p53 in response to DNA damage. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BAG6NM_001387994.1 linkuse as main transcriptc.109-717T>G intron_variant ENST00000676615.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BAG6ENST00000676615.2 linkuse as main transcriptc.109-717T>G intron_variant NM_001387994.1 A2P46379-3

Frequencies

GnomAD3 genomes
AF:
0.444
AC:
67317
AN:
151622
Hom.:
15622
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.592
Gnomad AMI
AF:
0.329
Gnomad AMR
AF:
0.423
Gnomad ASJ
AF:
0.336
Gnomad EAS
AF:
0.384
Gnomad SAS
AF:
0.311
Gnomad FIN
AF:
0.499
Gnomad MID
AF:
0.411
Gnomad NFE
AF:
0.372
Gnomad OTH
AF:
0.429
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.444
AC:
67373
AN:
151740
Hom.:
15637
Cov.:
30
AF XY:
0.446
AC XY:
33029
AN XY:
74130
show subpopulations
Gnomad4 AFR
AF:
0.592
Gnomad4 AMR
AF:
0.423
Gnomad4 ASJ
AF:
0.336
Gnomad4 EAS
AF:
0.384
Gnomad4 SAS
AF:
0.310
Gnomad4 FIN
AF:
0.499
Gnomad4 NFE
AF:
0.372
Gnomad4 OTH
AF:
0.427
Alfa
AF:
0.371
Hom.:
16653
Bravo
AF:
0.449
Asia WGS
AF:
0.363
AC:
1261
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.0
DANN
Benign
0.68

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: rs805301; hg19: chr6-31618121; API