22-26925209-T-C

Position:

• chr22-26925209-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.561 in 152,104 control chromosomes in the GnomAD database, including 27,325 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 0.56 (27325 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26925209T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01422	ENST00000670559.1	n.336-24490T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85272 AN: 151986 Hom.: 27265 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.561 AC: 85393 AN: 152104 Hom.: 27325 Cov.: 32 AF XY: 0.561 AC XY: 41716 AN XY: 74338

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.597

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.531

Alfa AF: 0.527 Hom.: 3560

Bravo AF: 0.578

Asia WGS AF: 0.555 AC: 1931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2213758; hg19: chr22-27321172;