rs703193

chr6-136288212-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCLAF1	NM_014739.3	c.-115+1501G>A		intron_variant		ENST00000531224.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCLAF1	ENST00000531224.6	c.-115+1501G>A		intron_variant		1	NM_014739.3	P4

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

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.250

Alfa AF: 0.219 Hom.: 722

Bravo AF: 0.262

Asia WGS AF: 0.270 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.97
Dann	Benign	0.25

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

Publications

LitVar

Other links and lift over

dbSNP: rs703193; hg19: chr6-136609350;