rs17369571

chr13-21913486-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 0.196 in 152,140 control chromosomes in the GnomAD database, including 3,138 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 0.20 (3138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 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: 0.196 AC: 29815 AN: 152022 Hom.: 3132 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.196 AC: 29844 AN: 152140 Hom.: 3138 Cov.: 32 AF XY: 0.192 AC XY: 14274 AN XY: 74400

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.197

Alfa AF: 0.184 Hom.: 4282

Bravo AF: 0.194

Asia WGS AF: 0.100 AC: 348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.35
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17369571; hg19: chr13-22487625;