chr14-22533736-G-T

Position:

• chr14-22533736-G-T

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 0.855 in 152,172 control chromosomes in the GnomAD database, including 56,262 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 0.86 (56262 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129990 AN: 152054 Hom.: 56197 Cov.: 31

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.855 AC: 130116 AN: 152172 Hom.: 56262 Cov.: 31 AF XY: 0.847 AC XY: 63033 AN XY: 74382

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.850

Gnomad4 EAS AF: 0.473

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.868

Alfa AF: 0.834 Hom.: 61108

Bravo AF: 0.858

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.5

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1154155; hg19: chr14-23002684;