rs10151103

Variant names:

• chr14-68868725-T-C
• rs10151103
• ENST00000553776.1:n.569A>G

Variant summary

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

The ENST00000553776.1(BLZF2P):​n.569A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.713 in 540,356 control chromosomes in the GnomAD database, including 139,336 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 0.69 (36055 hom., cov: 30)
  • Exomes 𝑓: 0.72 (103281 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.28
• Publications: 2 publications found

Genes affected

BLZF2P (HGNC:20049): (basic leucine zipper nuclear factor 2, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553776.1. 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
	BLZF2P	ENST00000553776.1	TSL:6	n.569A>G		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104065 AN: 150852 Hom.: 36024 Cov.: 30

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.692

GnomAD4 exome AF: 0.722 AC: 280960 AN: 389386 Hom.: 103281 Cov.: 0 AF XY: 0.722 AC XY: 156543 AN XY: 216930

African (AFR) AF: 0.695 AC: 6728 AN: 9678

American (AMR) AF: 0.819 AC: 21705 AN: 26498

Ashkenazi Jewish (ASJ) AF: 0.751 AC: 8394 AN: 11180

East Asian (EAS) AF: 0.518 AC: 9965 AN: 19234

South Asian (SAS) AF: 0.756 AC: 38314 AN: 50672

European-Finnish (FIN) AF: 0.692 AC: 20478 AN: 29574

Middle Eastern (MID) AF: 0.703 AC: 2094 AN: 2978

European-Non Finnish (NFE) AF: 0.723 AC: 158862 AN: 219736

Other (OTH) AF: 0.727 AC: 14420 AN: 19836

GnomAD4 genome AF: 0.690 AC: 104141 AN: 150970 Hom.: 36055 Cov.: 30 AF XY: 0.691 AC XY: 50855 AN XY: 73638

African (AFR) AF: 0.676 AC: 27794 AN: 41128

American (AMR) AF: 0.769 AC: 11667 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2509 AN: 3466

East Asian (EAS) AF: 0.500 AC: 2546 AN: 5088

South Asian (SAS) AF: 0.750 AC: 3606 AN: 4806

European-Finnish (FIN) AF: 0.665 AC: 6926 AN: 10410

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 46811 AN: 67632

Other (OTH) AF: 0.695 AC: 1459 AN: 2098

Alfa AF: 0.687 Hom.: 4520

Bravo AF: 0.695

Asia WGS AF: 0.702 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	9.2
DANN	Benign	0.63
PhyloP100		5.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10151103;

hg19: chr14-69335442;