rs2040692

Variant names:

• chr22-17350923-C-T
• rs2040692

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 0.505 in 151,650 control chromosomes in the GnomAD database, including 19,685 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 0.50 (19685 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 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: 0.505 AC: 76470 AN: 151534 Hom.: 19656 Cov.: 30

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.505 AC: 76567 AN: 151650 Hom.: 19685 Cov.: 30 AF XY: 0.513 AC XY: 37984 AN XY: 74038

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.504

Alfa AF: 0.474 Hom.: 36465

Bravo AF: 0.495

Asia WGS AF: 0.653 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040692; hg19: chr22-17831813;