chr6-136261359-G-T

Variant names:

• chr6-136261359-G-T
• rs62431284
• NM_014739.3:c.2663C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_014739.3(BCLAF1):​c.2663C>A​(p.Thr888Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BCLAF1 NM_014739.3 missense
• Clinical Significance: Benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 8.14
• Publications: 24 publications found

Genes affected

BCLAF1 (HGNC:16863): (BCL2 associated transcription factor 1) This gene encodes a transcriptional repressor that interacts with several members of the BCL2 family of proteins. Overexpression of this protein induces apoptosis, which can be suppressed by co-expression of BCL2 proteins. The protein localizes to dot-like structures throughout the nucleus, and redistributes to a zone near the nuclear envelope in cells undergoing apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.004388064).
• BP6: Variant 6-136261359-G-T is Benign according to our data. Variant chr6-136261359-G-T is described in ClinVar as Benign. ClinVar VariationId is 402420.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCLAF1	NM_014739.3	c.2663C>A	p.Thr888Asn	missense_variant	Exon 12 of 13	ENST00000531224.6	NP_055554.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCLAF1	ENST00000531224.6	c.2663C>A	p.Thr888Asn	missense_variant	Exon 12 of 13	1	NM_014739.3	ENSP00000435210.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.497 AC: 123282 AN: 247866 AF XY: 0.498

Gnomad AFR exome AF: 0.474

Gnomad AMR exome AF: 0.499

Gnomad ASJ exome AF: 0.499

Gnomad EAS exome AF: 0.500

Gnomad FIN exome AF: 0.500

Gnomad NFE exome AF: 0.498

Gnomad OTH exome AF: 0.499

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.904 Hom.: 40904

ExAC AF: 0.497 AC: 60398

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency (fails inbreeding filter)

BCLAF1-related disorder Benign:1

Apr 16, 2020

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Benign	-0.079	T
BayesDel_noAF	Benign	-0.35
CADD	Pathogenic	28
DANN	Uncertain	0.99
DEOGEN2	Benign	0.26	T;.;.;.;.;.
Eigen	Uncertain	0.62
Eigen_PC	Pathogenic	0.68
LIST_S2	Uncertain	0.95	D;D;D;D;D;.
MetaRNN	Benign	0.0044	T;T;T;T;T;T
MetaSVM	Benign	-0.82	T
MutationAssessor	Benign	1.1	L;.;.;.;.;.
PhyloP100		8.1
PrimateAI	Pathogenic	0.87	D
PROVEAN	Benign	-1.3	N;N;N;N;N;N
Sift	Uncertain	0.024	D;T;D;D;D;T
Sift4G	Uncertain	0.020	D;D;D;D;D;D
Vest4		0.92
ClinPred		0.014	T
GERP RS		5.5
Varity_R		0.14
gMVP		0.079
Mutation Taster		=78/22	polymorphism

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: rs62431284; hg19: chr6-136582497; COSMIC: COSV50356777;