20-1724828-C-T

Variant names:

• chr20-1724828-C-T
• rs202518
• ENST00000844954.1:n.357-2316G>A

Variant summary

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

The ENST00000844954.1(ENSG00000286288):​n.357-2316G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,916 control chromosomes in the GnomAD database, including 11,346 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 0.37 (11346 hom., cov: 32)
• Consequence: ENSG00000286288 ENST00000844954.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 1 publications found

Genes affected

ENSG00000286288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.443 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
ENSG00000286288	ENST00000844954.1	n.357-2316G>A		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56849 AN: 151800 Hom.: 11334 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.375 AC: 56898 AN: 151916 Hom.: 11346 Cov.: 32 AF XY: 0.371 AC XY: 27587 AN XY: 74262

African (AFR) AF: 0.251 AC: 10385 AN: 41432

American (AMR) AF: 0.450 AC: 6864 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3464

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5168

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4824

European-Finnish (FIN) AF: 0.359 AC: 3783 AN: 10542

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30350 AN: 67924

Other (OTH) AF: 0.360 AC: 759 AN: 2108

Alfa AF: 0.392 Hom.: 6500

Bravo AF: 0.376

Asia WGS AF: 0.281 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.61
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs202518; hg19: chr20-1705474;