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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGL4P1		n.32387314C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;