rs2212158

Variant names:

• chr22-15659538-A-G
• rs2212158

Variant summary

Our verdict is Likely benign. The variant received -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: LOC124905152 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 0 publications found

Genes affected

LOC124905152 (HGNC:48656): (mediator complex subunit 15 pseudogene 7)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.496 AC: 72930 AN: 147014 Hom.: 394 Cov.: 69

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

African (AFR) AF: 0.491 AC: 19416 AN: 39542

American (AMR) AF: 0.489 AC: 7198 AN: 14712

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1663 AN: 3364

East Asian (EAS) AF: 0.526 AC: 2672 AN: 5084

South Asian (SAS) AF: 0.512 AC: 2378 AN: 4646

European-Finnish (FIN) AF: 0.499 AC: 5189 AN: 10396

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 32854 AN: 66128

Other (OTH) AF: 0.494 AC: 1018 AN: 2060

Alfa AF: 0.499 Hom.: 94

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.14
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2212158;

hg19: chr14-19522923;