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.

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.*18G>C		downstream_gene	N/A

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 v4.9

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;