rs2212158

Positions:

• chr22-15659538-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 (395 hom., cov: 69)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.15659538A>G		intergenic_region
LOC124905152		n.15659538A>G		intragenic_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 72930 AN: 147014 Hom.: 394 Cov.: 69 FAILED QC

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.492

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.496 AC: 72983 AN: 147130 Hom.: 395 Cov.: 69 AF XY: 0.497 AC XY: 35742 AN XY: 71974

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.494

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.494

Alfa AF: 0.499 Hom.: 94

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2212158; hg19: chr14-19522923;