2-17284745-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000447321.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZFYVE9P2	ENST00000447321.1	TSL:6	n.454T>C		non_coding_transcript_exon	Exon 1 of 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

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1976809;

hg19: chr2-17466012;