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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.799 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

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.779

Alfa AF: 0.767 Hom.: 5587

Bravo AF: 0.804

Asia WGS AF: 0.754 AC: 2576 AN: 3418

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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