rs526654

Variant names:

• chr12-5095077-T-C
• rs526654

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 0.499 in 151,892 control chromosomes in the GnomAD database, including 19,013 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 0.50 (19013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 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: 0.499 AC: 75678 AN: 151774 Hom.: 18991 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.499 AC: 75743 AN: 151892 Hom.: 19013 Cov.: 32 AF XY: 0.502 AC XY: 37268 AN XY: 74254

African (AFR) AF: 0.496 AC: 20513 AN: 41376

American (AMR) AF: 0.448 AC: 6850 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1910 AN: 5140

South Asian (SAS) AF: 0.527 AC: 2533 AN: 4810

European-Finnish (FIN) AF: 0.589 AC: 6218 AN: 10562

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34513 AN: 67944

Other (OTH) AF: 0.460 AC: 970 AN: 2108

Alfa AF: 0.507 Hom.: 10055

Bravo AF: 0.483

Asia WGS AF: 0.466 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.42
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs526654; hg19: chr12-5204243;