chr20-1031383-C-A

Position:

• chr20-1031383-C-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_Moderate BA1

The ENST00000664648.1(ENSG00000286787):​n.299+1G>T variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0538 in 152,202 control chromosomes in the GnomAD database, including 315 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 0.054 (315 hom., cov: 32)
• Consequence: ENSG00000286787 ENST00000664648.1 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1031383C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286787	ENST00000664648.1	n.299+1G>T		splice_donor_variant, intron_variant

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8194 AN: 152084 Hom.: 315 Cov.: 32

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.0885

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0506

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

GnomAD4 genome AF: 0.0538 AC: 8190 AN: 152202 Hom.: 315 Cov.: 32 AF XY: 0.0520 AC XY: 3870 AN XY: 74424

Gnomad4 AFR AF: 0.0154

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.0260

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0128

Gnomad4 FIN AF: 0.0885

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0715 Hom.: 613

Bravo AF: 0.0492

Asia WGS AF: 0.00953 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11696364; hg19: chr20-1012026;