rs17433871

Variant names:

• chr1-22689610-T-C
• rs17433871

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 151,846 control chromosomes in the GnomAD database, including 4,069 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 (4069 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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: 0.225 AC: 34132 AN: 151728 Hom.: 4064 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.225 AC: 34151 AN: 151846 Hom.: 4069 Cov.: 31 AF XY: 0.220 AC XY: 16339 AN XY: 74196

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.250

Alfa AF: 0.260 Hom.: 7809

Bravo AF: 0.220

Asia WGS AF: 0.221 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17433871; hg19: chr1-23016103;