6-31650984-G-A

Position:

• chr6-31650984-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387994.1(BAG6):​c.108+672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,266 control chromosomes in the GnomAD database, including 61,072 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 0.89 (61072 hom., cov: 32)
• Consequence: BAG6 NM_001387994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAG6	NM_001387994.1	c.108+672C>T		intron_variant		ENST00000676615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAG6	ENST00000676615.2	c.108+672C>T		intron_variant			NM_001387994.1	A2

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136113 AN: 152148 Hom.: 61012 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.912

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.895 AC: 136232 AN: 152266 Hom.: 61072 Cov.: 32 AF XY: 0.896 AC XY: 66692 AN XY: 74444

Gnomad4 AFR AF: 0.930

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.859

Gnomad4 OTH AF: 0.913

Alfa AF: 0.873 Hom.: 103580

Bravo AF: 0.901

Asia WGS AF: 0.961 AC: 3344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.6
DANN	Benign	0.24

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

Other links and lift over

dbSNP: rs3130050; hg19: chr6-31618761;