rs17450784

Positions:

• chr5-109680925-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;