rs4809590

Positions:

• chr20-46456188-G-A

Variant summary

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

The ENST00000400371.2(ENSG00000293461):​n.1692C>T 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 0.174 in 153,588 control chromosomes in the GnomAD database, including 2,592 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 0.17 (2585 hom., cov: 33)
  • Exomes 𝑓: 0.080 (7 hom.)
• Consequence: ENST00000400371.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

(HGNC:):

ZNF663P (HGNC:25342): (zinc finger protein 663, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000400371.2	n.1692C>T		non_coding_transcript_exon_variant	3/4	1
ZNF663P	ENST00000641770.1	n.898C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26584 AN: 152040 Hom.: 2584 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0802

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.0796 AC: 114 AN: 1432 Hom.: 7 Cov.: 0 AF XY: 0.0825 AC XY: 63 AN XY: 764

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0700

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.175 AC: 26602 AN: 152156 Hom.: 2585 Cov.: 33 AF XY: 0.170 AC XY: 12668 AN XY: 74372

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0801

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.164

Alfa AF: 0.163 Hom.: 1165

Bravo AF: 0.188

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	12
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4809590; hg19: chr20-45084827; COSMIC: COSV68531023;