20-63586261-A-G

Variant names:

• chr20-63586261-A-G
• rs311498

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 0.921 in 152,222 control chromosomes in the GnomAD database, including 64,631 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 0.92 (64631 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.921 AC: 140103 AN: 152102 Hom.: 64578 Cov.: 33

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.959

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.921 AC: 140215 AN: 152222 Hom.: 64631 Cov.: 33 AF XY: 0.919 AC XY: 68421 AN XY: 74430

African (AFR) AF: 0.906 AC: 37605 AN: 41516

American (AMR) AF: 0.940 AC: 14384 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.959 AC: 3329 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5161 AN: 5162

South Asian (SAS) AF: 0.974 AC: 4704 AN: 4828

European-Finnish (FIN) AF: 0.866 AC: 9177 AN: 10602

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62848 AN: 68022

Other (OTH) AF: 0.926 AC: 1954 AN: 2110

Alfa AF: 0.927 Hom.: 93470

Bravo AF: 0.924

Asia WGS AF: 0.967 AC: 3364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.79
DANN	Benign	0.59
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs311498; hg19: chr20-62217614;