rs743400

Variant names:

• chr6-31639334-A-G
• rs743400
• NM_001387994.1:c.3394-108T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31639334-A-G
• chr6-31639334-A-T

Variant summary

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

The NM_001388012.1(BAG6):​c.3421-108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0615 in 1,434,778 control chromosomes in the GnomAD database, including 3,534 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 0.077 (649 hom., cov: 32)
  • Exomes 𝑓: 0.060 (2885 hom.)
• Consequence: BAG6 NM_001388012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 12 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001388012.1. 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.3394-108T>C		intron	N/A	NP_001374923.1
	BAG6	NM_001388012.1		c.3421-108T>C		intron	N/A	NP_001374941.1
	BAG6	NM_001387989.1		c.3394-108T>C		intron	N/A	NP_001374918.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAG6	ENST00000676615.2	MANE Select	c.3394-108T>C		intron	N/A	ENSP00000502941.1
	BAG6	ENST00000211379.9	TSL:1	c.3286-108T>C		intron	N/A	ENSP00000211379.5
	BAG6	ENST00000375976.8	TSL:1	c.3286-108T>C		intron	N/A	ENSP00000365143.4

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11658 AN: 151980 Hom.: 648 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0972

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.00643

Gnomad FIN AF: 0.00482

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0833

GnomAD4 exome AF: 0.0597 AC: 76578 AN: 1282680 Hom.: 2885 Cov.: 19 AF XY: 0.0571 AC XY: 36519 AN XY: 639432

African (AFR) AF: 0.138 AC: 4038 AN: 29174

American (AMR) AF: 0.0671 AC: 2632 AN: 39252

Ashkenazi Jewish (ASJ) AF: 0.0412 AC: 910 AN: 22098

East Asian (EAS) AF: 0.000908 AC: 35 AN: 38554

South Asian (SAS) AF: 0.00851 AC: 653 AN: 76754

European-Finnish (FIN) AF: 0.00776 AC: 397 AN: 51172

Middle Eastern (MID) AF: 0.0321 AC: 149 AN: 4648

European-Non Finnish (NFE) AF: 0.0668 AC: 64633 AN: 967306

Other (OTH) AF: 0.0583 AC: 3131 AN: 53722

GnomAD4 genome AF: 0.0766 AC: 11656 AN: 152098 Hom.: 649 Cov.: 32 AF XY: 0.0728 AC XY: 5414 AN XY: 74358

African (AFR) AF: 0.139 AC: 5761 AN: 41474

American (AMR) AF: 0.0971 AC: 1483 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5178

South Asian (SAS) AF: 0.00623 AC: 30 AN: 4818

European-Finnish (FIN) AF: 0.00482 AC: 51 AN: 10582

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0582 AC: 3957 AN: 67992

Other (OTH) AF: 0.0820 AC: 173 AN: 2110

Alfa AF: 0.0688 Hom.: 953

Bravo AF: 0.0888

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.74
PhyloP100		1.1
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: rs743400; hg19: chr6-31607111;