20-58800253-T-C

Variant names:

• chr20-58800253-T-C
• rs2145477
• ENST00000790561.1:n.24-3078A>G

Variant summary

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

The ENST00000790561.1(ENSG00000302935):​n.24-3078A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,062 control chromosomes in the GnomAD database, including 45,903 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 0.78 (45903 hom., cov: 31)
• Consequence: ENSG00000302935 ENST00000790561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 4 publications found

Genes affected

ENSG00000302935 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790561.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302935	ENST00000790561.1		n.24-3078A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117856 AN: 151944 Hom.: 45888 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.775 AC: 117917 AN: 152062 Hom.: 45903 Cov.: 31 AF XY: 0.776 AC XY: 57698 AN XY: 74334

African (AFR) AF: 0.839 AC: 34816 AN: 41480

American (AMR) AF: 0.718 AC: 10968 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2570 AN: 3472

East Asian (EAS) AF: 0.804 AC: 4154 AN: 5168

South Asian (SAS) AF: 0.769 AC: 3700 AN: 4810

European-Finnish (FIN) AF: 0.773 AC: 8167 AN: 10566

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51060 AN: 67974

Other (OTH) AF: 0.742 AC: 1566 AN: 2110

Alfa AF: 0.769 Hom.: 5590

Bravo AF: 0.776

Asia WGS AF: 0.730 AC: 2540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.72
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2145477; hg19: chr20-57375308;