rs17001543

chr22-23420962-C-G

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 0.0454 in 151,490 control chromosomes in the GnomAD database, including 206 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 0.045 (206 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0712 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: 0.0454 AC: 6870 AN: 151424 Hom.: 204 Cov.: 32

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0677

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0452

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0400

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

GnomAD4 genome AF: 0.0454 AC: 6877 AN: 151490 Hom.: 206 Cov.: 32 AF XY: 0.0457 AC XY: 3382 AN XY: 73932

Gnomad4 AFR AF: 0.0733

Gnomad4 AMR AF: 0.0313

Gnomad4 ASJ AF: 0.0202

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0690

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0358

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0386 Hom.: 19

Bravo AF: 0.0455

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.4
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17001543; hg19: chr22-23763149;