chr22-17726847-A-T

Variant names:

• chr22-17726847-A-T
• rs4488761
• NM_015367.4:c.771A>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_015367.4(BCL2L13):​c.771A>T​(p.Ser257Ser) variant causes a synonymous 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: BCL2L13 NM_015367.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 33 publications found

Genes affected

BCL2L13 (HGNC:17164): (BCL2 like 13) This gene encodes a mitochondrially-localized protein with conserved B-cell lymphoma 2 homology motifs. Overexpression of the encoded protein results in apoptosis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP7: Synonymous conserved (PhyloP=-0.629 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015367.4. 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
	BCL2L13	NM_015367.4	MANE Select	c.771A>T	p.Ser257Ser	synonymous	Exon 7 of 7	NP_056182.2
	BCL2L13	NM_001270733.2		c.-70A>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 2	NP_001257662.1
	BCL2L13	NM_001270726.1		c.843A>T	p.Ser281Ser	synonymous	Exon 6 of 6	NP_001257655.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL2L13	ENST00000317582.10	TSL:1 MANE Select	c.771A>T	p.Ser257Ser	synonymous	Exon 7 of 7	ENSP00000318883.5
	BCL2L13	ENST00000399777.2	TSL:1	n.*269A>T		non_coding_transcript_exon	Exon 6 of 6	ENSP00000382677.2
	BCL2L13	ENST00000355028.4	TSL:1	c.*41A>T		3_prime_UTR	Exon 5 of 5	ENSP00000347133.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 66

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.67
DANN	Benign	0.59
PhyloP100		-0.63

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: rs4488761; hg19: chr22-18209613;