14-68869414-T-C

Variant names:

• chr14-68869414-T-C
• rs4902660

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 0.701 in 149,262 control chromosomes in the GnomAD database, including 36,407 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 0.70 (36231 hom., cov: 28)
  • Exomes 𝑓: 0.78 (176 hom.)
• Consequence: BLZF2P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 1 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.769 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.223-51A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.701 AC: 104206 AN: 148602 Hom.: 36202 Cov.: 28

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.679

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.706

GnomAD4 exome AF: 0.780 AC: 426 AN: 546 Hom.: 176 AF XY: 0.772 AC XY: 247 AN XY: 320

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 0.833 AC: 10 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 13 AN: 14

East Asian (EAS) AF: 0.450 AC: 9 AN: 20

South Asian (SAS) AF: 0.911 AC: 51 AN: 56

European-Finnish (FIN) AF: 0.688 AC: 11 AN: 16

Middle Eastern (MID) AF: 1.00 AC: 4 AN: 4

European-Non Finnish (NFE) AF: 0.765 AC: 300 AN: 392

Other (OTH) AF: 0.867 AC: 26 AN: 30

GnomAD4 genome AF: 0.701 AC: 104277 AN: 148716 Hom.: 36231 Cov.: 28 AF XY: 0.704 AC XY: 50937 AN XY: 72332

African (AFR) AF: 0.690 AC: 27819 AN: 40306

American (AMR) AF: 0.781 AC: 11725 AN: 15018

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2508 AN: 3452

East Asian (EAS) AF: 0.533 AC: 2570 AN: 4822

South Asian (SAS) AF: 0.764 AC: 3598 AN: 4710

European-Finnish (FIN) AF: 0.694 AC: 6786 AN: 9778

Middle Eastern (MID) AF: 0.662 AC: 192 AN: 290

European-Non Finnish (NFE) AF: 0.697 AC: 46975 AN: 67380

Other (OTH) AF: 0.709 AC: 1460 AN: 2058

Alfa AF: 0.687 Hom.: 4366

Bravo AF: 0.695

Asia WGS AF: 0.701 AC: 2414 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	6.5
DANN	Benign	0.18
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs4902660; hg19: chr14-69336131;