chr20-1815815-G-T

Variant names:

• chr20-1815815-G-T
• rs200888
• ENST00000447206.1:n.38+1754C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000447206.1(ENSG00000286288):​n.38+1754C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,042 control chromosomes in the GnomAD database, including 7,401 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 0.28 (7401 hom., cov: 32)
• Consequence: ENSG00000286288 ENST00000447206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.68

Genes affected

ENSG00000286288 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 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	ENST00000447206.1	n.38+1754C>A		intron_variant	Intron 1 of 3	2
ENSG00000286288	ENST00000654380.1	n.80+1754C>A		intron_variant	Intron 1 of 2
ENSG00000286288	ENST00000658107.1	n.91+1754C>A		intron_variant	Intron 1 of 5
ENSG00000286288	ENST00000661517.1	n.197+1754C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42540 AN: 151922 Hom.: 7404 Cov.: 32

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.280 AC: 42533 AN: 152042 Hom.: 7401 Cov.: 32 AF XY: 0.282 AC XY: 20960 AN XY: 74312

Gnomad4 AFR AF: 0.0708

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.266

Alfa AF: 0.362 Hom.: 14182

Bravo AF: 0.257

Asia WGS AF: 0.349 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	21
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200888; hg19: chr20-1796461;