rs6018946

Positions:

• chr20-37502683-T-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

BLCAP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.37502683T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BLCAP	ENST00000613961.1	n.1293A>T		non_coding_transcript_exon_variant	1/1	6
BLCAP	ENST00000411780.1	n.128+6421A>T		intron_variant		3
BLCAP	ENST00000467603.1	n.299-129A>T		intron_variant		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

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

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

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.411

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6018946; hg19: chr20-36131085;