chr20-56256281-G-A

Variant names:

• chr20-56256281-G-A
• rs1926065

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.400 AC: 16571 AN: 41472

American (AMR) AF: 0.215 AC: 3282 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1053 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1540 AN: 5156

South Asian (SAS) AF: 0.328 AC: 1582 AN: 4818

European-Finnish (FIN) AF: 0.203 AC: 2144 AN: 10568

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19904 AN: 68002

Other (OTH) AF: 0.276 AC: 583 AN: 2114

Alfa AF: 0.291 Hom.: 12492

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs1926065; hg19: chr20-54831337;