6-31651799-A-G

Variant names:

• chr6-31651799-A-G
• rs3117583
• ENST00000456286.5:c.-36T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456286.5(BAG6):​c.-36T>C variant causes a 5 prime UTR 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 ENST00000456286.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455
• Publications: 52 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456286.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAG6	NM_001387994.1	MANE Select	c.-13-23T>C		intron	N/A	NP_001374923.1
	BAG6	NM_001388012.1		c.-13-23T>C		intron	N/A	NP_001374941.1
	BAG6	NM_001387989.1		c.-13-23T>C		intron	N/A	NP_001374918.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAG6	ENST00000456286.5	TSL:1	c.-36T>C		5_prime_UTR	Exon 1 of 6	ENSP00000406436.1
	BAG6	ENST00000676615.2	MANE Select	c.-13-23T>C		intron	N/A	ENSP00000502941.1
	BAG6	ENST00000211379.9	TSL:1	c.-13-23T>C		intron	N/A	ENSP00000211379.5

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

GnomAD2 exomes AF: 0.145 AC: 35657 AN: 246262 AF XY: 0.145

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 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

African (AFR) AF: 0.206 AC: 6812 AN: 33008

American (AMR) AF: 0.0802 AC: 3586 AN: 44690

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 3094 AN: 26006

East Asian (EAS) AF: 0.0465 AC: 1839 AN: 39566

South Asian (SAS) AF: 0.115 AC: 9863 AN: 85808

European-Finnish (FIN) AF: 0.161 AC: 8390 AN: 52270

Middle Eastern (MID) AF: 0.0923 AC: 514 AN: 5568

European-Non Finnish (NFE) AF: 0.192 AC: 209409 AN: 1092128

Other (OTH) AF: 0.165 AC: 9836 AN: 59610

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

African (AFR) AF: 0.193 AC: 8009 AN: 41506

American (AMR) AF: 0.0985 AC: 1505 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3468

East Asian (EAS) AF: 0.0791 AC: 410 AN: 5184

South Asian (SAS) AF: 0.124 AC: 600 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1704 AN: 10586

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12503 AN: 67984

Other (OTH) AF: 0.149 AC: 314 AN: 2112

Alfa AF: 0.178 Hom.: 8400

Bravo AF: 0.166

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.42
PhyloP100		0.46
PromoterAI		-0.085	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3117583; hg19: chr6-31619576;