20-2239664-A-T

Variant names:

• chr20-2239664-A-T
• rs59586681
• ENST00000651531.1:c.-48-18290A>T

Variant summary

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

The ENST00000651531.1(ENSG00000286022):​c.-48-18290A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,348 control chromosomes in the GnomAD database, including 9,251 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 0.34 (9251 hom., cov: 30)
• Consequence: ENSG00000286022 ENST00000651531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 10 publications found

Genes affected

ENSG00000286022 (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 (NFE) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286022	ENST00000651531.1	c.-48-18290A>T		intron_variant	Intron 1 of 13			ENSP00000498584.1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51410 AN: 151232 Hom.: 9241 Cov.: 30

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.340 AC: 51451 AN: 151348 Hom.: 9251 Cov.: 30 AF XY: 0.336 AC XY: 24845 AN XY: 73900

African (AFR) AF: 0.259 AC: 10676 AN: 41248

American (AMR) AF: 0.273 AC: 4139 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1322 AN: 3462

East Asian (EAS) AF: 0.116 AC: 595 AN: 5140

South Asian (SAS) AF: 0.341 AC: 1631 AN: 4786

European-Finnish (FIN) AF: 0.392 AC: 4086 AN: 10422

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27841 AN: 67798

Other (OTH) AF: 0.333 AC: 699 AN: 2102

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.327

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.31
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs59586681; hg19: chr20-2220310;