20-45495883-A-G

Variant names:

• chr20-45495883-A-G
• rs11696501
• ENST00000803561.1:n.119+8173A>G

Variant summary

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

The ENST00000803561.1(ENSG00000237464):​n.119+8173A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 149,334 control chromosomes in the GnomAD database, including 3,741 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 0.21 (3741 hom., cov: 29)
• Consequence: ENSG00000237464 ENST00000803561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.959
• Publications: 20 publications found

Genes affected

ENSG00000237464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803561.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237464	ENST00000803561.1		n.119+8173A>G		intron	N/A
	ENSG00000237464	ENST00000803562.1		n.126+8173A>G		intron	N/A
	ENSG00000237464	ENST00000803563.1		n.151+8173A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.214 AC: 31994 AN: 149216 Hom.: 3728 Cov.: 29

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.215 AC: 32041 AN: 149334 Hom.: 3741 Cov.: 29 AF XY: 0.215 AC XY: 15598 AN XY: 72688

African (AFR) AF: 0.206 AC: 8322 AN: 40472

American (AMR) AF: 0.258 AC: 3836 AN: 14842

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 737 AN: 3446

East Asian (EAS) AF: 0.419 AC: 2128 AN: 5074

South Asian (SAS) AF: 0.215 AC: 985 AN: 4578

European-Finnish (FIN) AF: 0.203 AC: 2065 AN: 10176

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.196 AC: 13249 AN: 67492

Other (OTH) AF: 0.219 AC: 451 AN: 2058

Alfa AF: 0.205 Hom.: 10582

Bravo AF: 0.225

Asia WGS AF: 0.305 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.79
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs11696501; hg19: chr20-44124523;