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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372555	XR_937312.3	n.355+3394T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309956	ENST00000846222.1	n.373+3394T>G		intron_variant	Intron 1 of 3
ENSG00000309956	ENST00000846223.1	n.357+3394T>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs6082126; hg19: chr20-20713651;