rs317089

Variant names:

• chr6-153200219-A-G
• rs317089

Your query was ambiguous. Multiple possible variants found:

• chr6-153200219-A-G
• chr6-153200219-A-T

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 0.898 in 152,296 control chromosomes in the GnomAD database, including 61,473 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 0.90 (61473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136640 AN: 152178 Hom.: 61428 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.918

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.898 AC: 136741 AN: 152296 Hom.: 61473 Cov.: 33 AF XY: 0.898 AC XY: 66900 AN XY: 74464

African (AFR) AF: 0.877 AC: 36460 AN: 41552

American (AMR) AF: 0.861 AC: 13177 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3011 AN: 3470

East Asian (EAS) AF: 0.790 AC: 4093 AN: 5180

South Asian (SAS) AF: 0.883 AC: 4256 AN: 4822

European-Finnish (FIN) AF: 0.970 AC: 10309 AN: 10626

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62442 AN: 68026

Other (OTH) AF: 0.876 AC: 1851 AN: 2114

Alfa AF: 0.901 Hom.: 10258

Bravo AF: 0.887

Asia WGS AF: 0.873 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.69
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs317089; hg19: chr6-153521354;