chr6-31650344-A-C

Position:

• chr6-31650344-A-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

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=-0.85).
• 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	Protein	UniProt
BAG6	NM_001387994.1	c.109-717T>G		intron_variant		ENST00000676615.2	NP_001374923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAG6	ENST00000676615.2	c.109-717T>G		intron_variant			NM_001387994.1	ENSP00000502941	A2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67317 AN: 151622 Hom.: 15622 Cov.: 30

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

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

Other links and lift over

dbSNP: rs805301; hg19: chr6-31618121;