rs10139069

Variant names:

• chr14-68868721-G-A
• rs10139069
• ENST00000553776.1:n.573C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-68868721-G-A
• chr14-68868721-G-T

Variant summary

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

The ENST00000553776.1(BLZF2P):​n.573C>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 0.702 in 529,442 control chromosomes in the GnomAD database, including 132,740 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 0.66 (33233 hom., cov: 29)
  • Exomes 𝑓: 0.72 (99507 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34
• 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=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.749 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BLZF2P	ENST00000553776.1	TSL:6	n.573C>T		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.661 AC: 99574 AN: 150752 Hom.: 33202 Cov.: 29

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.672

GnomAD4 exome AF: 0.719 AC: 272259 AN: 378574 Hom.: 99507 Cov.: 0 AF XY: 0.719 AC XY: 151843 AN XY: 211218

African (AFR) AF: 0.603 AC: 5622 AN: 9326

American (AMR) AF: 0.818 AC: 21287 AN: 26012

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 8066 AN: 10706

East Asian (EAS) AF: 0.524 AC: 9691 AN: 18508

South Asian (SAS) AF: 0.745 AC: 36680 AN: 49264

European-Finnish (FIN) AF: 0.693 AC: 19826 AN: 28602

Middle Eastern (MID) AF: 0.699 AC: 2047 AN: 2930

European-Non Finnish (NFE) AF: 0.725 AC: 155099 AN: 213928

Other (OTH) AF: 0.722 AC: 13941 AN: 19298

GnomAD4 genome AF: 0.661 AC: 99652 AN: 150868 Hom.: 33233 Cov.: 29 AF XY: 0.661 AC XY: 48666 AN XY: 73584

African (AFR) AF: 0.575 AC: 23634 AN: 41138

American (AMR) AF: 0.760 AC: 11521 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2507 AN: 3464

East Asian (EAS) AF: 0.500 AC: 2536 AN: 5072

South Asian (SAS) AF: 0.732 AC: 3516 AN: 4804

European-Finnish (FIN) AF: 0.668 AC: 6927 AN: 10364

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 46766 AN: 67584

Other (OTH) AF: 0.676 AC: 1419 AN: 2098

Alfa AF: 0.662 Hom.: 4014

Bravo AF: 0.661

Asia WGS AF: 0.683 AC: 2372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.7
DANN	Benign	0.43
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs10139069; hg19: chr14-69335438;