rs17698444

chr1-217243213-C-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 0.105 in 152,152 control chromosomes in the GnomAD database, including 925 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 0.10 (925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 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: 0.105 AC: 15951 AN: 152034 Hom.: 923 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0930

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

GnomAD4 genome AF: 0.105 AC: 15963 AN: 152152 Hom.: 925 Cov.: 32 AF XY: 0.105 AC XY: 7832 AN XY: 74368

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0842

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0944

Alfa AF: 0.105 Hom.: 106

Bravo AF: 0.101

Asia WGS AF: 0.0770 AC: 268 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	13
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17698444; hg19: chr1-217416555;