22-32387314-C-T

Variant names:

• chr22-32387314-C-T
• rs6518774

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 0.0579 in 151,940 control chromosomes in the GnomAD database, including 263 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 0.058 (263 hom., cov: 32)
• Consequence: RGL4P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 2 publications found

Genes affected

RGL4P1 (HGNC:56833):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0817 is higher than 0.05.

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: 0.0579 AC: 8787 AN: 151830 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.0841

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.00348

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0591

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

GnomAD4 genome AF: 0.0579 AC: 8796 AN: 151940 Hom.: 263 Cov.: 32 AF XY: 0.0568 AC XY: 4218 AN XY: 74262

African (AFR) AF: 0.0840 AC: 3480 AN: 41424

American (AMR) AF: 0.0539 AC: 822 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0686 AC: 238 AN: 3468

East Asian (EAS) AF: 0.00349 AC: 18 AN: 5160

South Asian (SAS) AF: 0.0756 AC: 363 AN: 4804

European-Finnish (FIN) AF: 0.0288 AC: 304 AN: 10546

Middle Eastern (MID) AF: 0.0655 AC: 19 AN: 290

European-Non Finnish (NFE) AF: 0.0501 AC: 3405 AN: 67976

Other (OTH) AF: 0.0585 AC: 123 AN: 2104

Alfa AF: 0.0463 Hom.: 120

Bravo AF: 0.0597

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.92
DANN	Benign	0.39
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6518774; hg19: chr22-32783301;