rs17450784

Variant names:

• chr5-109680925-T-C
• rs17450784

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 0.0936 in 152,164 control chromosomes in the GnomAD database, including 723 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 0.094 (723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.117 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: 0.0937 AC: 14242 AN: 152048 Hom.: 723 Cov.: 32

Gnomad AFR AF: 0.0657

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0704

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.0936 AC: 14239 AN: 152164 Hom.: 723 Cov.: 32 AF XY: 0.0913 AC XY: 6791 AN XY: 74378

Gnomad4 AFR AF: 0.0655

Gnomad4 AMR AF: 0.0701

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0969

Alfa AF: 0.112 Hom.: 552

Bravo AF: 0.0892

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17450784; hg19: chr5-109016626;