20-20733008-T-G

Variant names:

• chr20-20733008-T-G
• rs6082126
• ENST00000846222.1:n.373+3394T>G

Variant summary

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

The ENST00000846222.1(ENSG00000309956):​n.373+3394T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.047 in 152,164 control chromosomes in the GnomAD database, including 266 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 0.047 (266 hom., cov: 32)
• Consequence: ENSG00000309956 ENST00000846222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 2 publications found

Genes affected

ENSG00000309956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846222.1. 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
	ENSG00000309956	ENST00000846222.1		n.373+3394T>G		intron	N/A
	ENSG00000309956	ENST00000846223.1		n.357+3394T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7124 AN: 152044 Hom.: 263 Cov.: 32

Gnomad AFR AF: 0.0298

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.0808

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0350

Gnomad NFE AF: 0.0397

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0470 AC: 7146 AN: 152164 Hom.: 266 Cov.: 32 AF XY: 0.0493 AC XY: 3665 AN XY: 74388

African (AFR) AF: 0.0300 AC: 1245 AN: 41508

American (AMR) AF: 0.0564 AC: 863 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3470

East Asian (EAS) AF: 0.164 AC: 851 AN: 5174

South Asian (SAS) AF: 0.0804 AC: 387 AN: 4812

European-Finnish (FIN) AF: 0.0753 AC: 797 AN: 10580

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0397 AC: 2701 AN: 68002

Other (OTH) AF: 0.0449 AC: 95 AN: 2114

Alfa AF: 0.0295 Hom.: 18

Bravo AF: 0.0443

Asia WGS AF: 0.115 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.61
PhyloP100		0.076

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6082126;

hg19: chr20-20713651;