ENST00000792273.1:n.154+1892C>T

Variant names:

• chr20-54112406-C-T
• rs210069
• ENST00000792273.1:n.154+1892C>T

Variant summary

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

The ENST00000792273.1(ENSG00000286587):​n.154+1892C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 152,092 control chromosomes in the GnomAD database, including 7,362 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 0.31 (7362 hom., cov: 32)
• Consequence: ENSG00000286587 ENST00000792273.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 5 publications found

Genes affected

ENSG00000286587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792273.1. 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
	ENSG00000286587	ENST00000792273.1		n.154+1892C>T		intron	N/A
	ENSG00000286587	ENST00000792274.1		n.144+1892C>T		intron	N/A
	ENSG00000286587	ENST00000792275.1		n.186+1892C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47137 AN: 151974 Hom.: 7356 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.310 AC: 47167 AN: 152092 Hom.: 7362 Cov.: 32 AF XY: 0.309 AC XY: 22998 AN XY: 74358

African (AFR) AF: 0.325 AC: 13476 AN: 41478

American (AMR) AF: 0.331 AC: 5067 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.238 AC: 826 AN: 3470

East Asian (EAS) AF: 0.466 AC: 2413 AN: 5176

South Asian (SAS) AF: 0.309 AC: 1490 AN: 4828

European-Finnish (FIN) AF: 0.283 AC: 2993 AN: 10564

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19871 AN: 67974

Other (OTH) AF: 0.302 AC: 637 AN: 2108

Alfa AF: 0.301 Hom.: 29619

Bravo AF: 0.316

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.58
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs210069; hg19: chr20-52728945;