rs17222842

Positions:

• chr13-30765980-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;