rs17389541

Variant names:

• chr1-209813827-A-G
• rs17389541

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 0.177 in 152,182 control chromosomes in the GnomAD database, including 2,647 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 0.18 (2647 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

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 (NFE) allele frequency at 95% confidence interval = 0.211 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: 0.177 AC: 26942 AN: 152064 Hom.: 2648 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.177 AC: 26946 AN: 152182 Hom.: 2647 Cov.: 33 AF XY: 0.178 AC XY: 13206 AN XY: 74394

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0907

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.170

Alfa AF: 0.204 Hom.: 4278

Bravo AF: 0.169

Asia WGS AF: 0.0990 AC: 346 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	1.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17389541; hg19: chr1-209987172;