rs5992507

Positions:

• chr22-20069935-A-G

Variant summary

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

The variant allele was found at a frequency of 0.133 in 152,312 control chromosomes in the GnomAD database, including 2,177 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 0.13 (2176 hom., cov: 33)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20069935A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000236540	ENST00000595864.5	n.291+36T>C		intron_variant		5
ENSG00000236540	ENST00000596334.5	n.599+36T>C		intron_variant		5
ENSG00000236540	ENST00000598339.5	n.552+36T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20270 AN: 152116 Hom.: 2168 Cov.: 33

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0823

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.167 AC: 13 AN: 78 Hom.: 1 Cov.: 0 AF XY: 0.161 AC XY: 10 AN XY: 62

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.177

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.133 AC: 20297 AN: 152234 Hom.: 2176 Cov.: 33 AF XY: 0.141 AC XY: 10529 AN XY: 74420

Gnomad4 AFR AF: 0.0453

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.0823

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.135

Alfa AF: 0.131 Hom.: 755

Bravo AF: 0.140

Asia WGS AF: 0.292 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5992507; hg19: chr22-20057458;