chr22-17350923-C-T

Variant names:

• chr22-17350923-C-T
• rs2040692

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 0.505 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.519 AC: 21465 AN: 41334

American (AMR) AF: 0.450 AC: 6821 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3653 AN: 5162

South Asian (SAS) AF: 0.529 AC: 2542 AN: 4806

European-Finnish (FIN) AF: 0.646 AC: 6788 AN: 10510

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31643 AN: 67914

Other (OTH) AF: 0.504 AC: 1063 AN: 2108

Alfa AF: 0.478 Hom.: 78297

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2040692; hg19: chr22-17831813;