rs4809590

Variant names:

• chr20-46456188-G-A
• rs4809590
• ENST00000400371.2:n.1692C>T

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000293461 ENST00000400371.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 4 publications found

Genes affected

ENSG00000293461 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293461	ENST00000400371.2	n.1692C>T		non_coding_transcript_exon_variant	Exon 3 of 4	1
ENSG00000283757	ENST00000472805.2	n.2721C>T		non_coding_transcript_exon_variant	Exon 5 of 5	5
ZNF663P	ENST00000641770.1	n.898C>T		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 12

European-Finnish (FIN) AF: 0.0700 AC: 89 AN: 1272

Middle Eastern (MID) AF: 0.357 AC: 5 AN: 14

European-Non Finnish (NFE) AF: 0.188 AC: 18 AN: 96

Other (OTH) AF: 0.0625 AC: 2 AN: 32

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

African (AFR) AF: 0.258 AC: 10702 AN: 41480

American (AMR) AF: 0.160 AC: 2451 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3472

East Asian (EAS) AF: 0.0801 AC: 415 AN: 5178

South Asian (SAS) AF: 0.105 AC: 508 AN: 4824

European-Finnish (FIN) AF: 0.0793 AC: 841 AN: 10606

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10454 AN: 67992

Other (OTH) AF: 0.164 AC: 346 AN: 2110

Alfa AF: 0.164 Hom.: 1285

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
PhyloP100		-0.79

Splicing

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

Other links and lift over

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