5-20940020-G-A

Position:

• chr5-20940020-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 0.583 in 151,972 control chromosomes in the GnomAD database, including 26,707 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 0.58 (26707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 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: 0.583 AC: 88581 AN: 151854 Hom.: 26672 Cov.: 32

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.583 AC: 88669 AN: 151972 Hom.: 26707 Cov.: 32 AF XY: 0.592 AC XY: 43945 AN XY: 74268

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.690

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.610

Alfa AF: 0.520 Hom.: 11939

Bravo AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9292961; hg19: chr5-20940129;