22-16912130-G-T

Position:

• chr22-16912130-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 0.472 in 149,192 control chromosomes in the GnomAD database, including 17,062 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 0.47 (17062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 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: 0.472 AC: 70323 AN: 149078 Hom.: 17058 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.472 AC: 70346 AN: 149192 Hom.: 17062 Cov.: 32 AF XY: 0.479 AC XY: 34907 AN XY: 72880

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.491

Alfa AF: 0.458 Hom.: 3415

Bravo AF: 0.464

Asia WGS AF: 0.550 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5748736; hg19: chr22-17393020;