20-46107215-A-G

Variant names:

• chr20-46107215-A-G
• rs6065926
• ENST00000758803.1:n.234+1543T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000758803.1(ENSG00000298900):​n.234+1543T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,214 control chromosomes in the GnomAD database, including 51,358 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 0.82 (51358 hom., cov: 32)
• Consequence: ENSG00000298900 ENST00000758803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840
• Publications: 25 publications found

Genes affected

ENSG00000298900 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758803.1. 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
	ENSG00000298900	ENST00000758803.1		n.234+1543T>C		intron	N/A
	ENSG00000298900	ENST00000758805.1		n.*211T>C		downstream_gene	N/A
	ENSG00000298900	ENST00000758806.1		n.*218T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124035 AN: 152096 Hom.: 51294 Cov.: 32

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.723

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.816 AC: 124157 AN: 152214 Hom.: 51358 Cov.: 32 AF XY: 0.813 AC XY: 60532 AN XY: 74416

African (AFR) AF: 0.949 AC: 39424 AN: 41560

American (AMR) AF: 0.805 AC: 12301 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2544 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5178 AN: 5186

South Asian (SAS) AF: 0.811 AC: 3912 AN: 4822

European-Finnish (FIN) AF: 0.722 AC: 7644 AN: 10580

Middle Eastern (MID) AF: 0.723 AC: 211 AN: 292

European-Non Finnish (NFE) AF: 0.744 AC: 50586 AN: 67994

Other (OTH) AF: 0.788 AC: 1665 AN: 2112

Alfa AF: 0.792 Hom.: 8381

Bravo AF: 0.830

Asia WGS AF: 0.919 AC: 3197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	17
DANN	Benign	0.65
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs6065926; hg19: chr20-44735854;