rs17189000

Variant names:

• chr1-211376090-G-A
• rs17189000

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0487 AC: 2018 AN: 41410

American (AMR) AF: 0.0964 AC: 1472 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 587 AN: 3472

East Asian (EAS) AF: 0.101 AC: 524 AN: 5166

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4810

European-Finnish (FIN) AF: 0.112 AC: 1178 AN: 10544

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10899 AN: 67960

Other (OTH) AF: 0.141 AC: 298 AN: 2110

Alfa AF: 0.0889 Hom.: 414

Bravo AF: 0.115

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.67
DANN	Benign	0.38
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs17189000; hg19: chr1-211549432;