rs17222842

Variant names:

• chr13-30765980-G-A
• rs17222842

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 0.0602 in 152,062 control chromosomes in the GnomAD database, including 362 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 0.060 (362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0864 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: 0.0603 AC: 9160 AN: 151944 Hom.: 362 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.0950

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0602 AC: 9153 AN: 152062 Hom.: 362 Cov.: 32 AF XY: 0.0602 AC XY: 4471 AN XY: 74308

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.0494

Gnomad4 ASJ AF: 0.0619

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0641

Gnomad4 FIN AF: 0.0950

Gnomad4 NFE AF: 0.0883

Gnomad4 OTH AF: 0.0624

Alfa AF: 0.0753 Hom.: 163

Bravo AF: 0.0540

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.095
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17222842; hg19: chr13-31340117;