Variant 22-21627960-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.318 in 155,396 control chromosomes in the GnomAD database, including 9,265 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 0.32 ( 9171 hom., cov: 32)

Exomes 𝑓: 0.20 ( 94 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 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:

0.320

AC:

48671

AN:

151886

Hom.:

9127

Cov.:

show subpopulations

Gnomad AFR

AF:

0.480

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.514

Gnomad SAS

AF:

0.397

Gnomad FIN

AF:

0.347

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.296

GnomAD4 exome

AF:

0.202

AC:

684

AN:

3392

Hom.:

AF XY:

0.208

AC XY:

351

AN XY:

1686

show subpopulations

Gnomad4 AFR exome

AF:

0.362

Gnomad4 AMR exome

AF:

0.293

Gnomad4 ASJ exome

AF:

0.196

Gnomad4 EAS exome

AF:

0.299

Gnomad4 SAS exome

AF:

0.406

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.171

Gnomad4 OTH exome

AF:

0.224

GnomAD4 genome

AF:

0.321

AC:

48769

AN:

152004

Hom.:

9171

Cov.:

AF XY:

0.332

AC XY:

24646

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.481

Gnomad4 AMR

AF:

0.364

Gnomad4 ASJ

AF:

0.242

Gnomad4 EAS

AF:

0.515

Gnomad4 SAS

AF:

0.394

Gnomad4 FIN

AF:

0.347

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.302

Alfa

AF:

0.225

Hom.:

4339

Bravo

AF:

0.331

Asia WGS

AF:

0.503

AC:

1750

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.42

DANN

Benign

0.51

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over