rs17450784

Variant names:

• chr5-109680925-T-C
• rs17450784

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 0.0936 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0655 AC: 2722 AN: 41526

American (AMR) AF: 0.0701 AC: 1072 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3472

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5176

South Asian (SAS) AF: 0.110 AC: 529 AN: 4818

European-Finnish (FIN) AF: 0.0992 AC: 1050 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8100 AN: 67980

Other (OTH) AF: 0.0969 AC: 205 AN: 2116

Alfa AF: 0.110 Hom.: 732

Bravo AF: 0.0892

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.65
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs17450784; hg19: chr5-109016626;