19-49673914-G-C

Variant names:

• chr19-49673914-G-C
• rs3745469
• NM_138639.2:c.*166G>C

Variant summary

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

The NM_138639.2(BCL2L12):​c.*166G>C variant causes a splice region 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. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BCL2L12 NM_138639.2 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 0 publications found

Genes affected

BCL2L12 (HGNC:13787): (BCL2 like 12) This gene encodes a member of a family of proteins containing a Bcl-2 homology domain 2 (BH2). The encoded protein is an anti-apoptotic factor that acts as an inhibitor of caspases 3 and 7 in the cytoplasm. In the nucleus, it binds to the p53 tumor suppressor protein, preventing its association with target genes. Overexpression of this gene has been detected in a number of different cancers. There is a pseudogene for this gene on chromosome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138639.2. 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
	BCL2L12	NM_138639.2	MANE Select	c.*166G>C		splice_region	Exon 7 of 7	NP_619580.2	Q9HB09-1
	BCL2L12	NM_138639.2	MANE Select	c.*166G>C		3_prime_UTR	Exon 7 of 7	NP_619580.2	Q9HB09-1
	BCL2L12	NM_001040668.2		c.*166G>C		splice_region	Exon 7 of 7	NP_001035758.2	Q9HB09-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L12	ENST00000246784.8	TSL:1 MANE Select	c.*166G>C		splice_region	Exon 7 of 7	ENSP00000246784.4	Q9HB09-1
	BCL2L12	ENST00000246785.7	TSL:1	c.*166G>C		splice_region	Exon 7 of 7	ENSP00000246785.3	Q9HB09-1
	BCL2L12	ENST00000619007.4	TSL:1	c.*137G>C		splice_region	Exon 6 of 6	ENSP00000483272.2	A0A0X8AT42

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 7

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.34
DANN	Benign	0.50
PhyloP100		-0.27

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: rs3745469; hg19: chr19-50177171;