rs6018946

Variant names:

• chr20-37502683-T-A
• rs6018946
• ENST00000613961.1:n.1293A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000613961.1(BLCAP):​n.1293A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,928 control chromosomes in the GnomAD database, including 15,304 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 0.44 (15304 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: BLCAP ENST00000613961.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• Publications: 5 publications found

Genes affected

BLCAP (HGNC:1055): (BLCAP apoptosis inducing factor) This gene encodes a protein that reduces cell growth by stimulating apoptosis. Alternative splicing and the use of alternative promoters result in multiple transcript variants encoding the same protein. This gene is imprinted in brain where different transcript variants are expressed from each parental allele. Transcript variants initiating from the upstream promoter are expressed preferentially from the maternal allele, while transcript variants initiating downstream of the interspersed NNAT gene (GeneID:4826) are expressed from the paternal allele. Transcripts at this locus may also undergo A to I editing, resulting in amino acid changes at three positions in the N-terminus of the protein. [provided by RefSeq, Nov 2015]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLCAP	ENST00000613961.1	n.1293A>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
BLCAP	ENST00000411780.1	n.128+6421A>T		intron_variant	Intron 1 of 2	3
BLCAP	ENST00000467603.1	n.299-129A>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66173 AN: 151802 Hom.: 15276 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.436 AC: 66256 AN: 151920 Hom.: 15304 Cov.: 31 AF XY: 0.439 AC XY: 32580 AN XY: 74232

African (AFR) AF: 0.584 AC: 24204 AN: 41438

American (AMR) AF: 0.451 AC: 6891 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3466

East Asian (EAS) AF: 0.427 AC: 2201 AN: 5156

South Asian (SAS) AF: 0.556 AC: 2677 AN: 4816

European-Finnish (FIN) AF: 0.385 AC: 4046 AN: 10502

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23914 AN: 67942

Other (OTH) AF: 0.411 AC: 867 AN: 2110

Alfa AF: 0.405 Hom.: 1634

Bravo AF: 0.444

Asia WGS AF: 0.512 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	17
DANN	Benign	0.89
PhyloP100		1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6018946; hg19: chr20-36131085;