20-56256281-G-A

Position:

• chr20-56256281-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 0.309 in 152,082 control chromosomes in the GnomAD database, including 7,572 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 0.31 (7572 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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: 0.309 AC: 46909 AN: 151964 Hom.: 7566 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.309 AC: 46944 AN: 152082 Hom.: 7572 Cov.: 33 AF XY: 0.303 AC XY: 22535 AN XY: 74328

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.276

Alfa AF: 0.288 Hom.: 8829

Bravo AF: 0.313

Asia WGS AF: 0.314 AC: 1095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1926065; hg19: chr20-54831337;