6-31651799-A-G

Position:

• chr6-31651799-A-G

Variant summary

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

The NM_001387994.1(BAG6):​c.-13-23T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,590,808 control chromosomes in the GnomAD database, including 26,329 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 0.17 (2373 hom., cov: 32)
  • Exomes 𝑓: 0.18 (23956 hom.)
• Consequence: BAG6 NM_001387994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAG6	NM_001387994.1	c.-13-23T>C		intron_variant		ENST00000676615.2	NP_001374923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAG6	ENST00000676615.2	c.-13-23T>C		intron_variant			NM_001387994.1	ENSP00000502941	A2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25650 AN: 152036 Hom.: 2373 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0988

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0785

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.150

GnomAD3 exomes AF: 0.145 AC: 35657 AN: 246262 Hom.: 2915 AF XY: 0.145 AC XY: 19456 AN XY: 134206

Gnomad AFR exome AF: 0.198

Gnomad AMR exome AF: 0.0766

Gnomad ASJ exome AF: 0.114

Gnomad EAS exome AF: 0.0961

Gnomad SAS exome AF: 0.109

Gnomad FIN exome AF: 0.159

Gnomad NFE exome AF: 0.177

Gnomad OTH exome AF: 0.141

GnomAD4 exome AF: 0.176 AC: 253343 AN: 1438654 Hom.: 23956 Cov.: 26 AF XY: 0.174 AC XY: 124518 AN XY: 716930

Gnomad4 AFR exome AF: 0.206

Gnomad4 AMR exome AF: 0.0802

Gnomad4 ASJ exome AF: 0.119

Gnomad4 EAS exome AF: 0.0465

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.161

Gnomad4 NFE exome AF: 0.192

Gnomad4 OTH exome AF: 0.165

GnomAD4 genome AF: 0.169 AC: 25650 AN: 152154 Hom.: 2373 Cov.: 32 AF XY: 0.164 AC XY: 12202 AN XY: 74358

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0985

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0791

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.149

Alfa AF: 0.171 Hom.: 4333

Bravo AF: 0.166

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.42

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: rs3117583; hg19: chr6-31619576;