rs1742498

Variant names:

• chr14-68868145-G-A
• rs1742498
• ENST00000553776.1:n.842C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-68868145-G-A
• chr14-68868145-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.842C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.712 in 1,170,736 control chromosomes in the GnomAD database, including 299,374 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 (36342 hom., cov: 32)
  • Exomes 𝑓: 0.72 (263032 hom.)
• Consequence: BLZF2P ENST00000553776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.77
• Publications: 4 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=-0.51).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLZF2P		n.68868145G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLZF2P	ENST00000553776.1	n.842C>T		non_coding_transcript_exon_variant	Exon 4 of 4	6

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104732 AN: 151688 Hom.: 36311 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.725

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.692

GnomAD4 exome AF: 0.716 AC: 729250 AN: 1018928 Hom.: 263032 Cov.: 14 AF XY: 0.715 AC XY: 376062 AN XY: 526016

African (AFR) AF: 0.691 AC: 17026 AN: 24628

American (AMR) AF: 0.808 AC: 34529 AN: 42724

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 16457 AN: 22712

East Asian (EAS) AF: 0.447 AC: 16502 AN: 36916

South Asian (SAS) AF: 0.755 AC: 58299 AN: 77246

European-Finnish (FIN) AF: 0.664 AC: 33815 AN: 50934

Middle Eastern (MID) AF: 0.706 AC: 3371 AN: 4774

European-Non Finnish (NFE) AF: 0.725 AC: 517626 AN: 714378

Other (OTH) AF: 0.709 AC: 31625 AN: 44616

GnomAD4 genome AF: 0.690 AC: 104808 AN: 151808 Hom.: 36342 Cov.: 32 AF XY: 0.691 AC XY: 51242 AN XY: 74178

African (AFR) AF: 0.677 AC: 27989 AN: 41370

American (AMR) AF: 0.771 AC: 11760 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.725 AC: 2509 AN: 3462

East Asian (EAS) AF: 0.500 AC: 2575 AN: 5152

South Asian (SAS) AF: 0.750 AC: 3606 AN: 4810

European-Finnish (FIN) AF: 0.664 AC: 6981 AN: 10520

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47076 AN: 67922

Other (OTH) AF: 0.695 AC: 1467 AN: 2110

Alfa AF: 0.693 Hom.: 13132

Bravo AF: 0.696

Asia WGS AF: 0.704 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	16
DANN	Benign	0.64
PhyloP100		6.8

Splicing

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

Other links and lift over

dbSNP: rs1742498; hg19: chr14-69334862;