rs17189000

Positions:

• chr1-211376090-G-A
• chr1-211376090-G-C

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 0.12 in 151,942 control chromosomes in the GnomAD database, including 1,330 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 0.12 (1330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18165 AN: 151824 Hom.: 1326 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.120 AC: 18182 AN: 151942 Hom.: 1330 Cov.: 32 AF XY: 0.119 AC XY: 8801 AN XY: 74264

Gnomad4 AFR AF: 0.0487

Gnomad4 AMR AF: 0.0964

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0780 Hom.: 148

Bravo AF: 0.115

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.67
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17189000; hg19: chr1-211549432;