rs750332

Variant names:

• chr6-31639273-C-T
• rs750332
• NM_001387994.1:c.3394-47G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31639273-C-T
• chr6-31639273-C-A
• chr6-31639273-C-G

Variant summary

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

The NM_001387994.1(BAG6):​c.3394-47G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.825 in 1,556,814 control chromosomes in the GnomAD database, including 531,227 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.81 (49894 hom., cov: 30)
  • Exomes 𝑓: 0.83 (481333 hom.)
• Consequence: BAG6 NM_001387994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 18 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387994.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAG6	NM_001387994.1	MANE Select	c.3394-47G>A		intron	N/A	NP_001374923.1	P46379-3
	BAG6	NM_001388012.1		c.3421-47G>A		intron	N/A	NP_001374941.1
	BAG6	NM_001387989.1		c.3394-47G>A		intron	N/A	NP_001374918.1	P46379-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAG6	ENST00000676615.2	MANE Select	c.3394-47G>A		intron	N/A	ENSP00000502941.1	P46379-3
	BAG6	ENST00000211379.9	TSL:1	c.3286-47G>A		intron	N/A	ENSP00000211379.5	P46379-2
	BAG6	ENST00000375976.8	TSL:1	c.3286-47G>A		intron	N/A	ENSP00000365143.4	P46379-2

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122773 AN: 151856 Hom.: 49839 Cov.: 30

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.817

GnomAD2 exomes AF: 0.838 AC: 190682 AN: 227424 AF XY: 0.838

Gnomad AFR exome AF: 0.727

Gnomad AMR exome AF: 0.873

Gnomad ASJ exome AF: 0.910

Gnomad EAS exome AF: 0.848

Gnomad FIN exome AF: 0.862

Gnomad NFE exome AF: 0.834

Gnomad OTH exome AF: 0.841

GnomAD4 exome AF: 0.827 AC: 1161369 AN: 1404840 Hom.: 481333 Cov.: 22 AF XY: 0.827 AC XY: 579217 AN XY: 700420

African (AFR) AF: 0.726 AC: 23109 AN: 31838

American (AMR) AF: 0.869 AC: 36790 AN: 42314

Ashkenazi Jewish (ASJ) AF: 0.904 AC: 23024 AN: 25470

East Asian (EAS) AF: 0.891 AC: 34573 AN: 38798

South Asian (SAS) AF: 0.823 AC: 68986 AN: 83828

European-Finnish (FIN) AF: 0.856 AC: 45218 AN: 52798

Middle Eastern (MID) AF: 0.768 AC: 3796 AN: 4942

European-Non Finnish (NFE) AF: 0.823 AC: 878089 AN: 1066608

Other (OTH) AF: 0.820 AC: 47784 AN: 58244

GnomAD4 genome AF: 0.809 AC: 122885 AN: 151974 Hom.: 49894 Cov.: 30 AF XY: 0.810 AC XY: 60181 AN XY: 74286

African (AFR) AF: 0.729 AC: 30198 AN: 41414

American (AMR) AF: 0.846 AC: 12936 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3130 AN: 3472

East Asian (EAS) AF: 0.853 AC: 4410 AN: 5168

South Asian (SAS) AF: 0.836 AC: 4025 AN: 4812

European-Finnish (FIN) AF: 0.868 AC: 9168 AN: 10560

Middle Eastern (MID) AF: 0.812 AC: 237 AN: 292

European-Non Finnish (NFE) AF: 0.827 AC: 56230 AN: 67952

Other (OTH) AF: 0.818 AC: 1721 AN: 2104

Alfa AF: 0.822 Hom.: 103165

Bravo AF: 0.805

Asia WGS AF: 0.870 AC: 3026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.65
PhyloP100		-0.24
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: rs750332; hg19: chr6-31607050; COSMIC: COSV52994184; COSMIC: COSV52994184;