chr20-39489863-A-G

Variant names:

• chr20-39489863-A-G
• rs6028457
• ENST00000774323.1:n.209+21441A>G

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000774323.1(ENSG00000300834):​n.209+21441A>G variant causes a intron change. The variant allele was found at a frequency of 0.579 in 152,126 control chromosomes in the GnomAD database, including 25,957 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 0.58 (25957 hom., cov: 33)
• Consequence: ENSG00000300834 ENST00000774323.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.62
• Publications: 2 publications found

Genes affected

ENSG00000300834 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774323.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300834	ENST00000774323.1		n.209+21441A>G		intron	N/A
	ENSG00000300834	ENST00000774324.1		n.86-13854A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.579 AC: 88030 AN: 152008 Hom.: 25932 Cov.: 33

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.579 AC: 88093 AN: 152126 Hom.: 25957 Cov.: 33 AF XY: 0.577 AC XY: 42933 AN XY: 74360

African (AFR) AF: 0.558 AC: 23138 AN: 41498

American (AMR) AF: 0.457 AC: 6981 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1812 AN: 3470

East Asian (EAS) AF: 0.539 AC: 2786 AN: 5166

South Asian (SAS) AF: 0.513 AC: 2469 AN: 4814

European-Finnish (FIN) AF: 0.639 AC: 6752 AN: 10570

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42148 AN: 68000

Other (OTH) AF: 0.583 AC: 1231 AN: 2112

Alfa AF: 0.572 Hom.: 4901

Bravo AF: 0.563

Asia WGS AF: 0.482 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	21
DANN	Benign	0.86
PhyloP100		4.6

Splicing

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

Other links and lift over

dbSNP: rs6028457; hg19: chr20-38118506;