20-37510570-T-G

Variant names:

• chr20-37510570-T-G
• rs3764718
• ENST00000467603.1:n.190-1358A>C

Variant summary

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

The ENST00000467603.1(BLCAP):​n.190-1358A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,144 control chromosomes in the GnomAD database, including 42,166 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 0.74 (42166 hom., cov: 27)
• Consequence: BLCAP ENST00000467603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000467603.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLCAP	ENST00000467603.1	TSL:3	n.190-1358A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112326 AN: 151026 Hom.: 42129 Cov.: 27

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.744 AC: 112415 AN: 151144 Hom.: 42166 Cov.: 27 AF XY: 0.749 AC XY: 55258 AN XY: 73756

African (AFR) AF: 0.686 AC: 28201 AN: 41088

American (AMR) AF: 0.695 AC: 10522 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2047 AN: 3458

East Asian (EAS) AF: 0.869 AC: 4454 AN: 5126

South Asian (SAS) AF: 0.806 AC: 3823 AN: 4746

European-Finnish (FIN) AF: 0.893 AC: 9342 AN: 10456

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51861 AN: 67840

Other (OTH) AF: 0.679 AC: 1418 AN: 2088

Alfa AF: 0.745 Hom.: 7087

Bravo AF: 0.723

Asia WGS AF: 0.833 AC: 2893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.67
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs3764718; hg19: chr20-36138972;