6-31646325-C-T

Position:

• chr6-31646325-C-T

Variant summary

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

The NM_001387994.1(BAG6):​c.918+69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 1,560,148 control chromosomes in the GnomAD database, including 497,819 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 0.76 (44043 hom., cov: 31)
  • Exomes 𝑓: 0.80 (453776 hom.)
• Consequence: BAG6 NM_001387994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAG6	NM_001387994.1	c.918+69G>A		intron_variant		ENST00000676615.2	NP_001374923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAG6	ENST00000676615.2	c.918+69G>A		intron_variant			NM_001387994.1	ENSP00000502941	A2

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114702 AN: 151908 Hom.: 44002 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.738

GnomAD4 exome AF: 0.801 AC: 1128203 AN: 1408122 Hom.: 453776 AF XY: 0.802 AC XY: 558155 AN XY: 696092

Gnomad4 AFR exome AF: 0.608

Gnomad4 AMR exome AF: 0.812

Gnomad4 ASJ exome AF: 0.764

Gnomad4 EAS exome AF: 0.845

Gnomad4 SAS exome AF: 0.808

Gnomad4 FIN exome AF: 0.854

Gnomad4 NFE exome AF: 0.804

Gnomad4 OTH exome AF: 0.781

GnomAD4 genome AF: 0.755 AC: 114789 AN: 152026 Hom.: 44043 Cov.: 31 AF XY: 0.759 AC XY: 56387 AN XY: 74332

Gnomad4 AFR AF: 0.612

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.739

Alfa AF: 0.799 Hom.: 73176

Bravo AF: 0.743

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.49
DANN	Benign	0.80

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: rs2242656; hg19: chr6-31614102;