rs17880288

chr22-35394330-A-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 0.0532 in 152,404 control chromosomes in the GnomAD database, including 257 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 0.053 (256 hom., cov: 32)
  • Exomes 𝑓: 0.022 (1 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0661 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: 0.0534 AC: 8077 AN: 151254 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0443

GnomAD4 exome AF: 0.0215 AC: 23 AN: 1068 Hom.: 1 AF XY: 0.0236 AC XY: 16 AN XY: 678

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0119

Gnomad4 NFE exome AF: 0.0269

Gnomad4 OTH exome AF: 0.0294

GnomAD4 genome AF: 0.0534 AC: 8088 AN: 151336 Hom.: 256 Cov.: 32 AF XY: 0.0522 AC XY: 3855 AN XY: 73818

Gnomad4 AFR AF: 0.0682

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.00426

Gnomad4 SAS AF: 0.0264

Gnomad4 FIN AF: 0.0519

Gnomad4 NFE AF: 0.0565

Gnomad4 OTH AF: 0.0435

Alfa AF: 0.0590 Hom.: 39

Bravo AF: 0.0523

Asia WGS AF: 0.0220 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17880288; hg19: chr22-35790323;