rs525479

Variant names:

• chr6-153951579-A-G
• rs525479

Your query was ambiguous. Multiple possible variants found:

• chr6-153951579-A-G
• chr6-153951579-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 0.799 in 152,062 control chromosomes in the GnomAD database, including 48,922 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 0.80 (48922 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 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: 0.799 AC: 121433 AN: 151946 Hom.: 48897 Cov.: 33

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.667

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.799 AC: 121505 AN: 152062 Hom.: 48922 Cov.: 33 AF XY: 0.802 AC XY: 59597 AN XY: 74334

African (AFR) AF: 0.888 AC: 36860 AN: 41516

American (AMR) AF: 0.832 AC: 12714 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2330 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3917 AN: 5182

South Asian (SAS) AF: 0.788 AC: 3803 AN: 4824

European-Finnish (FIN) AF: 0.823 AC: 8673 AN: 10542

Middle Eastern (MID) AF: 0.666 AC: 193 AN: 290

European-Non Finnish (NFE) AF: 0.745 AC: 50604 AN: 67934

Other (OTH) AF: 0.779 AC: 1646 AN: 2114

Alfa AF: 0.771 Hom.: 5887

Bravo AF: 0.804

Asia WGS AF: 0.754 AC: 2576 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs525479; hg19: chr6-154272714; COSMIC: COSV69477307;