rs181224

chr17-58113647-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 0.607 in 151,990 control chromosomes in the GnomAD database, including 30,632 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 0.61 (30632 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 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: 0.607 AC: 92251 AN: 151870 Hom.: 30636 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.607 AC: 92263 AN: 151990 Hom.: 30632 Cov.: 31 AF XY: 0.613 AC XY: 45513 AN XY: 74296

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.640

Alfa AF: 0.691 Hom.: 18707

Bravo AF: 0.588

Asia WGS AF: 0.810 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.9
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181224; hg19: chr17-56191008;