6-31642752-A-G

Position:

• chr6-31642752-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.2043+77T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 1,534,950 control chromosomes in the GnomAD database, including 184,268 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 0.45 (16023 hom., cov: 32)
  • Exomes 𝑓: 0.49 (168245 hom.)
• Consequence: BAG6 NM_001387994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

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]

BAG6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAG6	NM_001387994.1	c.2043+77T>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.2043+77T>C		intron_variant			NM_001387994.1	ENSP00000502941.1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68389 AN: 151972 Hom.: 16004 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.480

GnomAD4 exome AF: 0.490 AC: 677463 AN: 1382860 Hom.: 168245 Cov.: 26 AF XY: 0.495 AC XY: 341133 AN XY: 688558

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.507

Gnomad4 ASJ exome AF: 0.613

Gnomad4 EAS exome AF: 0.584

Gnomad4 SAS exome AF: 0.589

Gnomad4 FIN exome AF: 0.380

Gnomad4 NFE exome AF: 0.484

Gnomad4 OTH exome AF: 0.493

GnomAD4 genome AF: 0.450 AC: 68452 AN: 152090 Hom.: 16023 Cov.: 32 AF XY: 0.450 AC XY: 33423 AN XY: 74348

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.484

Alfa AF: 0.491 Hom.: 32451

Bravo AF: 0.452

Asia WGS AF: 0.597 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.64
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1077393; hg19: chr6-31610529; COSMIC: COSV52995163; COSMIC: COSV52995163;