rs5756520

Positions:

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

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 0.408 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.402

Alfa AF: 0.432 Hom.: 1789

Bravo AF: 0.395

Asia WGS AF: 0.475 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5756520; hg19: chr22-37508507;