20-6787030-C-G

Position:

• chr20-6787030-C-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 0.492 in 151,964 control chromosomes in the GnomAD database, including 18,808 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 0.49 (18808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.505 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: 0.492 AC: 74686 AN: 151846 Hom.: 18799 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.492 AC: 74718 AN: 151964 Hom.: 18808 Cov.: 32 AF XY: 0.493 AC XY: 36591 AN XY: 74272

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.520

Alfa AF: 0.359 Hom.: 953

Bravo AF: 0.487

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.2
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235754; hg19: chr20-6767677;