rs5756520

Variant names:

• chr22-37112467-G-A
• rs5756520

Your query was ambiguous. Multiple possible variants found:

• chr22-37112467-G-A
• chr22-37112467-G-C

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 0.408 in 151,944 control chromosomes in the GnomAD database, including 12,768 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 0.41 (12768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 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: 0.407 AC: 61863 AN: 151826 Hom.: 12737 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.408 AC: 61949 AN: 151944 Hom.: 12768 Cov.: 32 AF XY: 0.409 AC XY: 30329 AN XY: 74236

African (AFR) AF: 0.401 AC: 16633 AN: 41444

American (AMR) AF: 0.339 AC: 5178 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1396 AN: 3472

East Asian (EAS) AF: 0.353 AC: 1822 AN: 5158

South Asian (SAS) AF: 0.485 AC: 2337 AN: 4822

European-Finnish (FIN) AF: 0.437 AC: 4593 AN: 10522

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28757 AN: 67942

Other (OTH) AF: 0.402 AC: 846 AN: 2106

Alfa AF: 0.432 Hom.: 1868

Bravo AF: 0.395

Asia WGS AF: 0.475 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.39
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs5756520; hg19: chr22-37508507;