rs7693

Variant names:

• chr14-103557367-C-A
• rs7693
• NM_001015048.3:c.*2454G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-103557367-C-A
• chr14-103557367-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001015048.3(BAG5):​c.*2454G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: BAG5 NM_001015048.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 27 publications found

Genes affected

BAG5 (HGNC:941): (BAG cochaperone 5) The protein encoded by this gene is a member of the BAG1-related protein family. BAG1 is an anti-apoptotic protein that functions through interactions with a variety of cell apoptosis and growth related proteins including BCL-2, Raf-protein kinase, steroid hormone receptors, growth factor receptors and members of the heat shock protein 70 kDa family. This protein contains a BAG domain near the C-terminus, which could bind and inhibit the chaperone activity of Hsc70/Hsp70. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

BAG5 Gene-Disease associations (from GenCC):

• cardiomyopathy, dilated, 2F

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• dilated cardiomyopathy

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ENSG00000258851 (HGNC:58460):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001015048.3. 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
	BAG5	NM_001015048.3	MANE Select	c.*2454G>T		3_prime_UTR	Exon 2 of 2	NP_001015048.1	A0A024R6M6
	BAG5	NM_001015049.5		c.*2454G>T		3_prime_UTR	Exon 2 of 2	NP_001015049.2	A0A024R6M6
	BAG5	NM_004873.4		c.*2454G>T		3_prime_UTR	Exon 2 of 2	NP_004864.1	A0A024R6M6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAG5	ENST00000299204.6	TSL:1 MANE Select	c.*2454G>T		3_prime_UTR	Exon 2 of 2	ENSP00000299204.4	Q9UL15-1
	BAG5	ENST00000445922.2	TSL:1	c.*2454G>T		3_prime_UTR	Exon 2 of 2	ENSP00000391713.2	Q9UL15-1
	ENSG00000258851	ENST00000556332.1	TSL:4	n.442+3505C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 13037

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.76
DANN	Benign	0.53
PhyloP100		-0.39

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: rs7693; hg19: chr14-104023704;