20-4323230-C-G

Variant names:

• chr20-4323230-C-G
• rs2422925
• ENST00000755410.1:n.51-16685C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000755410.1(ENSG00000298420):​n.51-16685C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,188 control chromosomes in the GnomAD database, including 3,345 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 0.19 (3345 hom., cov: 32)
• Consequence: ENSG00000298420 ENST00000755410.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 2 publications found

Genes affected

ENSG00000298420 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 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
ENSG00000298420	ENST00000755410.1	n.51-16685C>G		intron_variant	Intron 1 of 3
ENSG00000298420	ENST00000755411.1	n.555-16685C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28497 AN: 152070 Hom.: 3345 Cov.: 32

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0860

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.179

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.187 AC: 28503 AN: 152188 Hom.: 3345 Cov.: 32 AF XY: 0.193 AC XY: 14360 AN XY: 74414

African (AFR) AF: 0.0554 AC: 2300 AN: 41530

American (AMR) AF: 0.256 AC: 3921 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 855 AN: 3470

East Asian (EAS) AF: 0.0866 AC: 448 AN: 5172

South Asian (SAS) AF: 0.269 AC: 1295 AN: 4818

European-Finnish (FIN) AF: 0.329 AC: 3481 AN: 10596

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15653 AN: 67998

Other (OTH) AF: 0.177 AC: 373 AN: 2110

Alfa AF: 0.216 Hom.: 472

Bravo AF: 0.173

Asia WGS AF: 0.170 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.1
DANN	Benign	0.76
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2422925; hg19: chr20-4303877;