rs17450420

Variant names:

• chr13-104386796-A-G
• rs17450420

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 0.0599 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0291 AC: 1210 AN: 41548

American (AMR) AF: 0.116 AC: 1777 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3468

East Asian (EAS) AF: 0.0404 AC: 209 AN: 5172

South Asian (SAS) AF: 0.0487 AC: 235 AN: 4828

European-Finnish (FIN) AF: 0.0594 AC: 629 AN: 10596

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4430 AN: 68006

Other (OTH) AF: 0.0771 AC: 163 AN: 2114

Alfa AF: 0.0654 Hom.: 956

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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs17450420; hg19: chr13-105039146;