chr14-22492115-A-G

Position:

• chr14-22492115-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 0.273 in 151,164 control chromosomes in the GnomAD database, including 5,966 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 0.27 (5966 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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 = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41309 AN: 151046 Hom.: 5968 Cov.: 27

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.273 AC: 41316 AN: 151164 Hom.: 5966 Cov.: 27 AF XY: 0.278 AC XY: 20502 AN XY: 73806

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.315

Alfa AF: 0.290 Hom.: 13256

Bravo AF: 0.265

Asia WGS AF: 0.440 AC: 1526 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	8.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2128997; hg19: chr14-22961102;