Variant 12-93677236-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 0.0618 in 152,248 control chromosomes in the GnomAD database, including 408 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 0.062 ( 408 hom., cov: 32)

Exomes 𝑓: 0.14 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

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=-0.64).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 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:

0.0616

AC:

9374

AN:

152118

Hom.:

402

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0390

Gnomad ASJ

AF:

0.0824

Gnomad EAS

AF:

0.0985

Gnomad SAS

AF:

0.0886

Gnomad FIN

AF:

0.0200

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0347

Gnomad OTH

AF:

0.0511

GnomAD4 exome

AF:

0.143

AC:

AN:

Hom.:

AF XY:

0.125

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.167

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0618

AC:

9409

AN:

152234

Hom.:

408

Cov.:

AF XY:

0.0608

AC XY:

4526

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.117

Gnomad4 AMR

AF:

0.0390

Gnomad4 ASJ

AF:

0.0824

Gnomad4 EAS

AF:

0.0989

Gnomad4 SAS

AF:

0.0885

Gnomad4 FIN

AF:

0.0200

Gnomad4 NFE

AF:

0.0347

Gnomad4 OTH

AF:

0.0521

Alfa

AF:

0.0425

Hom.:

163

Bravo

AF:

0.0647

Asia WGS

AF:

0.0800

AC:

276

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

0.19

DANN

Benign

0.87

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