22-27039858-G-A

Variant names:

• chr22-27039858-G-A
• rs742004

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 0.26 in 152,136 control chromosomes in the GnomAD database, including 5,912 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 0.26 (5912 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 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: 0.261 AC: 39619 AN: 152018 Hom.: 5913 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.260 AC: 39608 AN: 152136 Hom.: 5912 Cov.: 33 AF XY: 0.267 AC XY: 19826 AN XY: 74394

African (AFR) AF: 0.104 AC: 4301 AN: 41508

American (AMR) AF: 0.262 AC: 4003 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3470

East Asian (EAS) AF: 0.244 AC: 1262 AN: 5166

South Asian (SAS) AF: 0.345 AC: 1662 AN: 4818

European-Finnish (FIN) AF: 0.419 AC: 4438 AN: 10594

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22210 AN: 67968

Other (OTH) AF: 0.277 AC: 587 AN: 2116

Alfa AF: 0.230 Hom.: 1876

Bravo AF: 0.240

Asia WGS AF: 0.287 AC: 998 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	1.6
DANN	Benign	0.37
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs742004; hg19: chr22-27435820;