Variant 1-196972363-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 0.623 in 151,856 control chromosomes in the GnomAD database, including 31,162 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 0.62 ( 31162 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.412

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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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:

0.623

AC:

94583

AN:

151738

Hom.:

31115

Cov.:

show subpopulations

Gnomad AFR

AF:

0.811

Gnomad AMI

AF:

0.297

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.634

Gnomad EAS

AF:

0.890

Gnomad SAS

AF:

0.673

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.497

Gnomad OTH

AF:

0.628

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

GnomAD4 genome

AF:

0.623

AC:

94681

AN:

151856

Hom.:

31162

Cov.:

AF XY:

0.630

AC XY:

46755

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.811

Gnomad4 AMR

AF:

0.671

Gnomad4 ASJ

AF:

0.634

Gnomad4 EAS

AF:

0.890

Gnomad4 SAS

AF:

0.672

Gnomad4 FIN

AF:

0.503

Gnomad4 NFE

AF:

0.497

Gnomad4 OTH

AF:

0.626

Alfa

AF:

0.534

Hom.:

29854

Bravo

AF:

0.645

Asia WGS

AF:

0.767

AC:

2663

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

4.3

DANN

Benign

0.85

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