rs17222842

Variant names:

• chr13-30765980-G-A
• rs17222842

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 0.0602 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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0149 AC: 616 AN: 41464

American (AMR) AF: 0.0494 AC: 756 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.0641 AC: 309 AN: 4820

European-Finnish (FIN) AF: 0.0950 AC: 1004 AN: 10572

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0883 AC: 5998 AN: 67946

Other (OTH) AF: 0.0624 AC: 132 AN: 2116

Alfa AF: 0.0640 Hom.: 201

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17222842; hg19: chr13-31340117;