rs5752592

Variant names:

• chr22-27571691-G-A
• rs5752592
• ENST00000415655.1:n.66+1817C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000415655.1(ENSG00000224027):​n.66+1817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,012 control chromosomes in the GnomAD database, including 1,227 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 0.12 (1227 hom., cov: 31)
• Consequence: ENSG00000224027 ENST00000415655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

ENSG00000224027 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224027	ENST00000415655.1	n.66+1817C>T		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18242 AN: 151894 Hom.: 1221 Cov.: 31

Gnomad AFR AF: 0.0730

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0724

Gnomad ASJ AF: 0.0958

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.120 AC: 18256 AN: 152012 Hom.: 1227 Cov.: 31 AF XY: 0.118 AC XY: 8788 AN XY: 74288

Gnomad4 AFR AF: 0.0730

Gnomad4 AMR AF: 0.0723

Gnomad4 ASJ AF: 0.0958

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.112

Alfa AF: 0.138 Hom.: 2189

Bravo AF: 0.110

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5752592; hg19: chr22-27967652;