rs17106421

Variant names:

• chr14-68867839-C-G
• rs17106421

Variant summary

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

The variant allele was found at a frequency of 0.0574 in 381,058 control chromosomes in the GnomAD database, including 798 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 0.068 (393 hom., cov: 32)
  • Exomes 𝑓: 0.051 (405 hom.)
• Consequence: BLZF2P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BLZF2P		n.68867839C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BLZF2P	ENST00000553776.1	n.*18G>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.0677 AC: 10297 AN: 152084 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.0434

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0520

Gnomad OTH AF: 0.0722

GnomAD4 exome AF: 0.0505 AC: 11559 AN: 228856 Hom.: 405 Cov.: 0 AF XY: 0.0475 AC XY: 5926 AN XY: 124784

African (AFR) AF: 0.0814 AC: 459 AN: 5642

American (AMR) AF: 0.103 AC: 1117 AN: 10870

Ashkenazi Jewish (ASJ) AF: 0.0255 AC: 160 AN: 6282

East Asian (EAS) AF: 0.140 AC: 1666 AN: 11888

South Asian (SAS) AF: 0.0151 AC: 436 AN: 28788

European-Finnish (FIN) AF: 0.0380 AC: 591 AN: 15564

Middle Eastern (MID) AF: 0.0400 AC: 87 AN: 2174

European-Non Finnish (NFE) AF: 0.0471 AC: 6384 AN: 135438

Other (OTH) AF: 0.0540 AC: 659 AN: 12210

GnomAD4 genome AF: 0.0677 AC: 10300 AN: 152202 Hom.: 393 Cov.: 32 AF XY: 0.0670 AC XY: 4989 AN XY: 74422

African (AFR) AF: 0.0926 AC: 3843 AN: 41510

American (AMR) AF: 0.0884 AC: 1351 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.137 AC: 708 AN: 5184

South Asian (SAS) AF: 0.0155 AC: 75 AN: 4824

European-Finnish (FIN) AF: 0.0434 AC: 460 AN: 10588

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0520 AC: 3536 AN: 68016

Other (OTH) AF: 0.0733 AC: 155 AN: 2114

Alfa AF: 0.0575 Hom.: 36

Bravo AF: 0.0761

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.0
DANN	Benign	0.63
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs17106421; hg19: chr14-69334556;