chr20-58790220-A-G

Variant names:

• chr20-58790220-A-G
• rs911297
• ENST00000790561.1:n.251+5980T>C

Variant summary

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

The ENST00000790561.1(ENSG00000302935):​n.251+5980T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,170 control chromosomes in the GnomAD database, including 56,738 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 0.86 (56738 hom., cov: 31)
• Consequence: ENSG00000302935 ENST00000790561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• Publications: 3 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 = 0.958 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302935	ENST00000790561.1		n.251+5980T>C		intron	N/A
	ENSG00000302935	ENST00000790562.1		n.563+5980T>C		intron	N/A
	ENSG00000302935	ENST00000790563.1		n.572+5980T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130840 AN: 152052 Hom.: 56688 Cov.: 31

Gnomad AFR AF: 0.966

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.861 AC: 130948 AN: 152170 Hom.: 56738 Cov.: 31 AF XY: 0.858 AC XY: 63810 AN XY: 74366

African (AFR) AF: 0.966 AC: 40095 AN: 41522

American (AMR) AF: 0.789 AC: 12062 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2780 AN: 3472

East Asian (EAS) AF: 0.809 AC: 4174 AN: 5162

South Asian (SAS) AF: 0.834 AC: 4017 AN: 4816

European-Finnish (FIN) AF: 0.829 AC: 8776 AN: 10584

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56257 AN: 68002

Other (OTH) AF: 0.848 AC: 1792 AN: 2112

Alfa AF: 0.836 Hom.: 26949

Bravo AF: 0.862

Asia WGS AF: 0.819 AC: 2851 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	0.28
DANN	Benign	0.49
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs911297; hg19: chr20-57365275;