rs17330522

Variant names:

• chr13-23490130-C-A
• rs17330522

Your query was ambiguous. Multiple possible variants found:

• chr13-23490130-C-A
• chr13-23490130-C-G

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 0.0716 in 152,258 control chromosomes in the GnomAD database, including 503 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 0.072 (503 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 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: 0.0717 AC: 10904 AN: 152140 Hom.: 503 Cov.: 33

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0678

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

GnomAD4 genome AF: 0.0716 AC: 10903 AN: 152258 Hom.: 503 Cov.: 33 AF XY: 0.0708 AC XY: 5269 AN XY: 74436

African (AFR) AF: 0.0208 AC: 864 AN: 41548

American (AMR) AF: 0.0539 AC: 824 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3470

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0973 AC: 469 AN: 4820

European-Finnish (FIN) AF: 0.0849 AC: 900 AN: 10602

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.103 AC: 6989 AN: 68016

Other (OTH) AF: 0.0676 AC: 143 AN: 2116

Alfa AF: 0.0473 Hom.: 122

Bravo AF: 0.0659

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs17330522; hg19: chr13-24064269;