rs2040692

Positions:

• chr22-17350923-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;