20-6800984-C-T

Position:

• chr20-6800984-C-T

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 0.183 in 152,154 control chromosomes in the GnomAD database, including 3,741 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 0.18 (3741 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.652

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 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: 0.183 AC: 27801 AN: 152036 Hom.: 3734 Cov.: 33

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.183 AC: 27843 AN: 152154 Hom.: 3741 Cov.: 33 AF XY: 0.181 AC XY: 13501 AN XY: 74408

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.0955

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.165

Alfa AF: 0.147 Hom.: 551

Bravo AF: 0.199

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs235746; hg19: chr20-6781631;