20-58802045-A-G

Variant names:

• chr20-58802045-A-G
• rs6015375
• ENST00000790561.1:n.23+1617T>C

Variant summary

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

The ENST00000790561.1(ENSG00000302935):​n.23+1617T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,074 control chromosomes in the GnomAD database, including 46,323 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 (46323 hom., cov: 31)
• Consequence: ENSG00000302935 ENST00000790561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 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.23+1617T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118303 AN: 151956 Hom.: 46302 Cov.: 31

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.778 AC: 118370 AN: 152074 Hom.: 46323 Cov.: 31 AF XY: 0.778 AC XY: 57813 AN XY: 74324

African (AFR) AF: 0.860 AC: 35672 AN: 41482

American (AMR) AF: 0.720 AC: 11005 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2589 AN: 3472

East Asian (EAS) AF: 0.803 AC: 4138 AN: 5156

South Asian (SAS) AF: 0.689 AC: 3315 AN: 4814

European-Finnish (FIN) AF: 0.772 AC: 8157 AN: 10564

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 51006 AN: 67982

Other (OTH) AF: 0.746 AC: 1573 AN: 2108

Alfa AF: 0.773 Hom.: 14266

Bravo AF: 0.782

Asia WGS AF: 0.695 AC: 2419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs6015375; hg19: chr20-57377100;