20-39061842-A-G

Variant names:

• chr20-39061842-A-G
• rs926391
• ENST00000772862.1:n.281+10948A>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+10948A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,858 control chromosomes in the GnomAD database, including 22,360 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 (22360 hom., cov: 31)
• Consequence: ENSG00000300599 ENST00000772862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 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
ENSG00000300599	ENST00000772862.1	n.281+10948A>G		intron_variant	Intron 2 of 4
ENSG00000300599	ENST00000772863.1	n.203+10948A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80604 AN: 151740 Hom.: 22319 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.531 AC: 80704 AN: 151858 Hom.: 22360 Cov.: 31 AF XY: 0.531 AC XY: 39388 AN XY: 74218

African (AFR) AF: 0.698 AC: 28898 AN: 41416

American (AMR) AF: 0.545 AC: 8310 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1905 AN: 3472

East Asian (EAS) AF: 0.572 AC: 2950 AN: 5158

South Asian (SAS) AF: 0.509 AC: 2454 AN: 4822

European-Finnish (FIN) AF: 0.417 AC: 4388 AN: 10532

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30060 AN: 67888

Other (OTH) AF: 0.533 AC: 1123 AN: 2106

Alfa AF: 0.500 Hom.: 10372

Bravo AF: 0.553

Asia WGS AF: 0.609 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.40
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs926391; hg19: chr20-37690485;