rs17698444

Variant names:

• chr1-217243213-C-G
• rs17698444

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;