chr2-17284745-T-C

Variant names:

• chr2-17284745-T-C
• rs1976809
• ENST00000447321.1:n.454T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZFYVE9P2		n.17284745T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFYVE9P2	ENST00000447321.1	n.454T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.592 AC: 16111 AN: 27202

American (AMR) AF: 0.196 AC: 8385 AN: 42876

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 8859 AN: 23316

East Asian (EAS) AF: 0.0593 AC: 2197 AN: 37068

South Asian (SAS) AF: 0.504 AC: 38878 AN: 77114

European-Finnish (FIN) AF: 0.223 AC: 11507 AN: 51672

Middle Eastern (MID) AF: 0.404 AC: 2041 AN: 5048

European-Non Finnish (NFE) AF: 0.392 AC: 310967 AN: 793854

Other (OTH) AF: 0.387 AC: 18475 AN: 47728

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

African (AFR) AF: 0.581 AC: 24067 AN: 41440

American (AMR) AF: 0.279 AC: 4262 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1305 AN: 3466

East Asian (EAS) AF: 0.0507 AC: 262 AN: 5164

South Asian (SAS) AF: 0.486 AC: 2339 AN: 4812

European-Finnish (FIN) AF: 0.209 AC: 2210 AN: 10582

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25058 AN: 67976

Other (OTH) AF: 0.392 AC: 828 AN: 2110

Alfa AF: 0.377 Hom.: 46239

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
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1976809; hg19: chr2-17466012;