rs2844463

Variant names:

• chr6-31647390-G-A
• rs2844463
• NM_001387994.1:c.788+201C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 41 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=-0.87).
• 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 rank	MANE	Protein	UniProt
BAG6	NM_001387994.1	c.788+201C>T		intron_variant	Intron 7 of 25	ENST00000676615.2	NP_001374923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAG6	ENST00000676615.2	c.788+201C>T		intron_variant	Intron 7 of 25		NM_001387994.1	ENSP00000502941.1

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

African (AFR) AF: 0.472 AC: 19560 AN: 41402

American (AMR) AF: 0.202 AC: 3085 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1215 AN: 5172

South Asian (SAS) AF: 0.206 AC: 994 AN: 4826

European-Finnish (FIN) AF: 0.0906 AC: 960 AN: 10592

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8830 AN: 67976

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.177 Hom.: 10228

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
PhyloP100		-0.18
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: rs2844463; hg19: chr6-31615167; COSMIC: COSV52996852; COSMIC: COSV52996852;