rs5760590

Positions:

• chr22-24694801-G-A
• chr22-24694801-G-C

Variant summary

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

The ENST00000633827.2(ENSG00000282012):​n.173+1046C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,772 control chromosomes in the GnomAD database, including 27,772 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 0.60 (27772 hom., cov: 30)
• Consequence: ENSG00000282012 ENST00000633827.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836

Genes affected

ENSG00000282012 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905092	XR_007068025.1	n.187+1046C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000282012	ENST00000633827.2	n.173+1046C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90760 AN: 151654 Hom.: 27731 Cov.: 30

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.599 AC: 90855 AN: 151772 Hom.: 27772 Cov.: 30 AF XY: 0.598 AC XY: 44323 AN XY: 74138

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.581

Alfa AF: 0.547 Hom.: 29902

Bravo AF: 0.609

Asia WGS AF: 0.637 AC: 2216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	1.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5760590; hg19: chr22-25090768;