rs1976809

chr2-17284745-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447321.1(ZFYVE9P2):n.454T>C 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 0.38 in 1,257,910 control chromosomes in the GnomAD database, including 98,370 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 0.40 (13720 hom., cov: 32)
  • Exomes 𝑓: 0.38 (84650 hom.)
• Consequence: ZFYVE9P2 ENST00000447321.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

Genes affected

ZFYVE9P2 (HGNC:39046): (zinc finger FYVE-type containing 9 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZFYVE9P2	ENST00000447321.1	n.454T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60717 AN: 151914 Hom.: 13673 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.394

GnomAD4 exome AF: 0.377 AC: 417420 AN: 1105878 Hom.: 84650 Cov.: 21 AF XY: 0.381 AC XY: 215310 AN XY: 564638

Gnomad4 AFR exome AF: 0.592

Gnomad4 AMR exome AF: 0.196

Gnomad4 ASJ exome AF: 0.380

Gnomad4 EAS exome AF: 0.0593

Gnomad4 SAS exome AF: 0.504

Gnomad4 FIN exome AF: 0.223

Gnomad4 NFE exome AF: 0.392

Gnomad4 OTH exome AF: 0.387

GnomAD4 genome AF: 0.400 AC: 60812 AN: 152032 Hom.: 13720 Cov.: 32 AF XY: 0.392 AC XY: 29127 AN XY: 74324

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.0507

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.392

Alfa AF: 0.375 Hom.: 22486

Bravo AF: 0.406

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	11
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1976809; hg19: chr2-17466012;