Variant 22-36482113-G-T 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 0.583 in 148,838 control chromosomes in the GnomAD database, including 27,173 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 0.58 ( 27166 hom., cov: 22)

Exomes 𝑓: 0.52 ( 7 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.347

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 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:

0.583

AC:

86692

AN:

148684

Hom.:

27159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.388

Gnomad AMI

AF:

0.773

Gnomad AMR

AF:

0.678

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.343

Gnomad FIN

AF:

0.615

Gnomad MID

AF:

0.558

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.619

GnomAD4 exome

AF:

0.522

AC:

AN:

Hom.:

AF XY:

0.474

AC XY:

AN XY:

show subpopulations

Gnomad4 SAS exome

AF:

0.412

Gnomad4 NFE exome

AF:

0.833

GnomAD4 genome

AF:

0.583

AC:

86724

AN:

148792

Hom.:

27166

Cov.:

AF XY:

0.575

AC XY:

41660

AN XY:

72470

show subpopulations

Gnomad4 AFR

AF:

0.388

Gnomad4 AMR

AF:

0.679

Gnomad4 ASJ

AF:

0.589

Gnomad4 EAS

AF:

0.254

Gnomad4 SAS

AF:

0.344

Gnomad4 FIN

AF:

0.615

Gnomad4 NFE

AF:

0.712

Gnomad4 OTH

AF:

0.615

Alfa

AF:

0.624

Hom.:

4435

Bravo

AF:

0.585

Asia WGS

AF:

0.327

AC:

1138

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

2.4

DANN

Benign

0.65

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