Variant 2-223974979-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 0.422 in 152,042 control chromosomes in the GnomAD database, including 14,093 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 0.42 ( 14093 hom., cov: 32)

Exomes 𝑓: 0.30 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.990

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 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:

0.421

AC:

64007

AN:

151914

Hom.:

14071

Cov.:

show subpopulations

Gnomad AFR

AF:

0.560

Gnomad AMI

AF:

0.500

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.413

Gnomad EAS

AF:

0.411

Gnomad SAS

AF:

0.346

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.350

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.415

GnomAD4 exome

AF:

0.300

AC:

AN:

Hom.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.333

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.422

AC:

64083

AN:

152032

Hom.:

14093

Cov.:

AF XY:

0.417

AC XY:

30974

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.561

Gnomad4 AMR

AF:

0.439

Gnomad4 ASJ

AF:

0.413

Gnomad4 EAS

AF:

0.411

Gnomad4 SAS

AF:

0.346

Gnomad4 FIN

AF:

0.271

Gnomad4 NFE

AF:

0.362

Gnomad4 OTH

AF:

0.417

Alfa

AF:

0.374

Hom.:

22446

Bravo

AF:

0.444

Asia WGS

AF:

0.384

AC:

1335

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

0.095

Dann

Benign

0.22

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