rs17450420

Positions:

• chr13-104386796-A-G

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 0.0599 in 152,220 control chromosomes in the GnomAD database, including 348 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 (348 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.112 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: 0.0599 AC: 9111 AN: 152102 Hom.: 347 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0401

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0594

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.0784

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

GnomAD4 genome AF: 0.0599 AC: 9114 AN: 152220 Hom.: 348 Cov.: 32 AF XY: 0.0617 AC XY: 4590 AN XY: 74406

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0404

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.0594

Gnomad4 NFE AF: 0.0651

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0696 Hom.: 398

Bravo AF: 0.0626

Asia WGS AF: 0.0570 AC: 198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17450420; hg19: chr13-105039146;