20-39061821-A-G

Variant names:

• chr20-39061821-A-G
• rs926392
• ENST00000772862.1:n.281+10927A>G

Variant summary

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

The ENST00000772862.1(ENSG00000300599):​n.281+10927A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,922 control chromosomes in the GnomAD database, including 22,244 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 0.53 (22244 hom., cov: 31)
• Consequence: ENSG00000300599 ENST00000772862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 12 publications found

Genes affected

ENSG00000300599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772862.1. 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
	ENSG00000300599	ENST00000772862.1		n.281+10927A>G		intron	N/A
	ENSG00000300599	ENST00000772863.1		n.203+10927A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80430 AN: 151804 Hom.: 22203 Cov.: 31

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.530 AC: 80531 AN: 151922 Hom.: 22244 Cov.: 31 AF XY: 0.529 AC XY: 39310 AN XY: 74248

African (AFR) AF: 0.696 AC: 28819 AN: 41434

American (AMR) AF: 0.544 AC: 8298 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1896 AN: 3468

East Asian (EAS) AF: 0.572 AC: 2951 AN: 5162

South Asian (SAS) AF: 0.508 AC: 2447 AN: 4818

European-Finnish (FIN) AF: 0.416 AC: 4386 AN: 10538

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 29995 AN: 67928

Other (OTH) AF: 0.532 AC: 1123 AN: 2112

Alfa AF: 0.472 Hom.: 53247

Bravo AF: 0.552

Asia WGS AF: 0.608 AC: 2112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.25
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs926392; hg19: chr20-37690464;