22-20666976-A-G

Variant names:

• chr22-20666976-A-G
• rs674478

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 0.167 in 152,140 control chromosomes in the GnomAD database, including 3,468 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 0.17 (3468 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.167 AC: 25331 AN: 152022 Hom.: 3462 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0469

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.0957

Gnomad FIN AF: 0.0616

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.167 AC: 25379 AN: 152140 Hom.: 3468 Cov.: 32 AF XY: 0.163 AC XY: 12124 AN XY: 74388

African (AFR) AF: 0.386 AC: 15988 AN: 41454

American (AMR) AF: 0.101 AC: 1544 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0469 AC: 163 AN: 3472

East Asian (EAS) AF: 0.0809 AC: 419 AN: 5182

South Asian (SAS) AF: 0.0968 AC: 467 AN: 4824

European-Finnish (FIN) AF: 0.0616 AC: 653 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0847 AC: 5759 AN: 68008

Other (OTH) AF: 0.143 AC: 302 AN: 2114

Alfa AF: 0.0814 Hom.: 408

Bravo AF: 0.178

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs674478; hg19: chr22-21021264;