NM_001387994.1:c.108+672C>T

Variant names:

• chr6-31650984-G-A
• rs3130050
• NM_001387994.1:c.108+672C>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.108+672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,266 control chromosomes in the GnomAD database, including 61,072 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 0.89 (61072 hom., cov: 32)
• Consequence: BAG6 NM_001387994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.714
• Publications: 42 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAG6	NM_001387994.1	MANE Select	c.108+672C>T		intron	N/A	NP_001374923.1
	BAG6	NM_001388012.1		c.108+672C>T		intron	N/A	NP_001374941.1
	BAG6	NM_001387989.1		c.108+672C>T		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.108+672C>T		intron	N/A	ENSP00000502941.1
	BAG6	ENST00000211379.9	TSL:1	c.108+672C>T		intron	N/A	ENSP00000211379.5
	BAG6	ENST00000375976.8	TSL:1	c.108+672C>T		intron	N/A	ENSP00000365143.4

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136113 AN: 152148 Hom.: 61012 Cov.: 32

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.912

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.895 AC: 136232 AN: 152266 Hom.: 61072 Cov.: 32 AF XY: 0.896 AC XY: 66692 AN XY: 74444

African (AFR) AF: 0.930 AC: 38623 AN: 41540

American (AMR) AF: 0.922 AC: 14106 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3305 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5141 AN: 5190

South Asian (SAS) AF: 0.899 AC: 4338 AN: 4826

European-Finnish (FIN) AF: 0.874 AC: 9271 AN: 10606

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58397 AN: 68020

Other (OTH) AF: 0.913 AC: 1931 AN: 2114

Alfa AF: 0.875 Hom.: 250041

Bravo AF: 0.901

Asia WGS AF: 0.961 AC: 3344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.6
DANN	Benign	0.24
PhyloP100		0.71
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: rs3130050; hg19: chr6-31618761;