rs17430279

chr2-184571535-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 0.225 in 152,056 control chromosomes in the GnomAD database, including 4,093 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 0.22 (4093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 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: 0.225 AC: 34142 AN: 151938 Hom.: 4087 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.238

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.225 AC: 34167 AN: 152056 Hom.: 4093 Cov.: 32 AF XY: 0.228 AC XY: 16940 AN XY: 74322

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.238

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.229

Alfa AF: 0.241 Hom.: 3963

Bravo AF: 0.208

Asia WGS AF: 0.263 AC: 912 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.1
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17430279; hg19: chr2-185436262;