rs17001543

Variant names:

• chr22-23420962-C-G
• rs17001543

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 0.0454 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0733 AC: 3028 AN: 41284

American (AMR) AF: 0.0313 AC: 477 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5158

South Asian (SAS) AF: 0.0690 AC: 331 AN: 4794

European-Finnish (FIN) AF: 0.0412 AC: 426 AN: 10328

Middle Eastern (MID) AF: 0.0420 AC: 12 AN: 286

European-Non Finnish (NFE) AF: 0.0358 AC: 2435 AN: 67942

Other (OTH) AF: 0.0397 AC: 83 AN: 2090

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs17001543; hg19: chr22-23763149;