rs2040699

Variant names:

• chr22-27646565-C-T
• rs2040699

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 0.208 in 152,088 control chromosomes in the GnomAD database, including 3,776 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 0.21 (3776 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.266 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: 0.208 AC: 31573 AN: 151970 Hom.: 3770 Cov.: 33

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.208 AC: 31583 AN: 152088 Hom.: 3776 Cov.: 33 AF XY: 0.209 AC XY: 15551 AN XY: 74336

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.218

Alfa AF: 0.251 Hom.: 6798

Bravo AF: 0.202

Asia WGS AF: 0.220 AC: 762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040699; hg19: chr22-28042532;