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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.898 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

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.790

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.918

Gnomad4 OTH AF: 0.876

Alfa AF: 0.902 Hom.: 9957

Bravo AF: 0.887

Asia WGS AF: 0.873 AC: 3038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs317089; hg19: chr6-153521354;