20-40130189-G-A

Position:

• chr20-40130189-G-A

Variant summary

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

The variant allele was found at a frequency of 0.447 in 151,976 control chromosomes in the GnomAD database, including 16,825 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 0.45 (16825 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67951 AN: 151858 Hom.: 16817 Cov.: 33

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.447 AC: 67987 AN: 151976 Hom.: 16825 Cov.: 33 AF XY: 0.449 AC XY: 33348 AN XY: 74302

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.471

Alfa AF: 0.502 Hom.: 5556

Bravo AF: 0.440

Asia WGS AF: 0.525 AC: 1825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.2
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs735998; hg19: chr20-38758830;