chr6-136288212-C-T

Variant names:

• chr6-136288212-C-T
• rs703193
• NM_014739.3:c.-115+1501G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014739.3(BCLAF1):​c.-115+1501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,130 control chromosomes in the GnomAD database, including 6,340 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 0.25 (6340 hom., cov: 33)
• Consequence: BCLAF1 NM_014739.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 5 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014739.3. 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
	BCLAF1	NM_014739.3	MANE Select	c.-115+1501G>A		intron	N/A	NP_055554.1
	BCLAF1	NM_001386700.1		c.-260+1501G>A		intron	N/A	NP_001373629.1
	BCLAF1	NM_001386701.1		c.-135+1501G>A		intron	N/A	NP_001373630.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCLAF1	ENST00000531224.6	TSL:1 MANE Select	c.-115+1501G>A		intron	N/A	ENSP00000435210.1
	BCLAF1	ENST00000527759.5	TSL:1	c.-115+1501G>A		intron	N/A	ENSP00000434826.1
	BCLAF1	ENST00000530767.5	TSL:1	c.-115+1501G>A		intron	N/A	ENSP00000436501.1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37927 AN: 152012 Hom.: 6303 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.250 AC: 38031 AN: 152130 Hom.: 6340 Cov.: 33 AF XY: 0.246 AC XY: 18307 AN XY: 74378

African (AFR) AF: 0.482 AC: 19975 AN: 41462

American (AMR) AF: 0.162 AC: 2475 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1236 AN: 5180

South Asian (SAS) AF: 0.181 AC: 874 AN: 4832

European-Finnish (FIN) AF: 0.148 AC: 1571 AN: 10582

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10581 AN: 67996

Other (OTH) AF: 0.250 AC: 529 AN: 2114

Alfa AF: 0.228 Hom.: 816

Bravo AF: 0.262

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.97
DANN	Benign	0.25
PhyloP100		-1.1
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: rs703193; hg19: chr6-136609350;