rs2844463

chr6-31647390-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.788+201C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,036 control chromosomes in the GnomAD database, including 6,062 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 0.24 (6062 hom., cov: 31)
• Consequence: BAG6 NM_001387994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAG6	NM_001387994.1	c.788+201C>T		intron_variant		ENST00000676615.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAG6	ENST00000676615.2	c.788+201C>T		intron_variant			NM_001387994.1	A2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36320 AN: 151918 Hom.: 6051 Cov.: 31

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.239 AC: 36354 AN: 152036 Hom.: 6062 Cov.: 31 AF XY: 0.237 AC XY: 17638 AN XY: 74350

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.0906

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.272

Alfa AF: 0.156 Hom.: 4336

Bravo AF: 0.259

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.1
Dann	Benign	0.64

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: rs2844463; hg19: chr6-31615167; COSMIC: COSV52996852; COSMIC: COSV52996852;