Variant 12-65966384-C-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 0.5 in 173,088 control chromosomes in the GnomAD database, including 22,691 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 0.49 ( 19260 hom., cov: 32)

Exomes 𝑓: 0.56 ( 3431 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.789

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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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:

0.493

AC:

74826

AN:

151916

Hom.:

19265

Cov.:

show subpopulations

Gnomad AFR

AF:

0.384

Gnomad AMI

AF:

0.529

Gnomad AMR

AF:

0.588

Gnomad ASJ

AF:

0.655

Gnomad EAS

AF:

0.810

Gnomad SAS

AF:

0.676

Gnomad FIN

AF:

0.486

Gnomad MID

AF:

0.570

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.527

GnomAD4 exome

AF:

0.560

AC:

11783

AN:

21054

Hom.:

3431

AF XY:

0.561

AC XY:

5492

AN XY:

9788

show subpopulations

Gnomad4 AFR exome

AF:

0.391

Gnomad4 AMR exome

AF:

0.557

Gnomad4 ASJ exome

AF:

0.640

Gnomad4 EAS exome

AF:

0.731

Gnomad4 SAS exome

AF:

0.713

Gnomad4 FIN exome

AF:

0.498

Gnomad4 NFE exome

AF:

0.505

Gnomad4 OTH exome

AF:

0.517

GnomAD4 genome

AF:

0.492

AC:

74840

AN:

152034

Hom.:

19260

Cov.:

AF XY:

0.500

AC XY:

37122

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.384

Gnomad4 AMR

AF:

0.587

Gnomad4 ASJ

AF:

0.655

Gnomad4 EAS

AF:

0.809

Gnomad4 SAS

AF:

0.676

Gnomad4 FIN

AF:

0.486

Gnomad4 NFE

AF:

0.491

Gnomad4 OTH

AF:

0.524

Alfa

AF:

0.461

Hom.:

2438

Bravo

AF:

0.499

Asia WGS

AF:

0.679

AC:

2358

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.91

DANN

Benign

0.67

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