20-5613786-T-G

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 0.714 in 152,186 control chromosomes in the GnomAD database, including 40,222 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 0.71 (40222 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108550 AN: 152068 Hom.: 40169 Cov.: 34

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.714 AC: 108658 AN: 152186 Hom.: 40222 Cov.: 34 AF XY: 0.707 AC XY: 52617 AN XY: 74390

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.707

Alfa AF: 0.663 Hom.: 5408

Bravo AF: 0.736

Asia WGS AF: 0.676 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.8
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6116869; hg19: chr20-5594432;