Variant 6-29636005-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 0.00629 in 1,478,756 control chromosomes in the GnomAD database, including 272 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 0.0060 ( 18 hom., cov: 32)

Exomes 𝑓: 0.0063 ( 254 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.548

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=-0.59).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0631 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:

0.00598

AC:

911

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000700

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00209

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.0693

Gnomad SAS

AF:

0.0549

Gnomad FIN

AF:

0.000942

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00263

Gnomad OTH

AF:

0.00621

GnomAD4 exome

AF:

0.00633

AC:

8396

AN:

1326424

Hom.:

254

AF XY:

0.00776

AC XY:

5172

AN XY:

666300

show subpopulations

Gnomad4 AFR exome

AF:

0.000587

Gnomad4 AMR exome

AF:

0.00169

Gnomad4 ASJ exome

AF:

0.00484

Gnomad4 EAS exome

AF:

0.0472

Gnomad4 SAS exome

AF:

0.0491

Gnomad4 FIN exome

AF:

0.00158

Gnomad4 NFE exome

AF:

0.00168

Gnomad4 OTH exome

AF:

0.00835

GnomAD4 genome

AF:

0.00597

AC:

909

AN:

152332

Hom.:

Cov.:

AF XY:

0.00726

AC XY:

541

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.000698

Gnomad4 AMR

AF:

0.00209

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.0690

Gnomad4 SAS

AF:

0.0550

Gnomad4 FIN

AF:

0.000942

Gnomad4 NFE

AF:

0.00263

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.00344

Hom.:

Bravo

AF:

0.00550

Asia WGS

AF:

0.0540

AC:

187

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

7.6

DANN

Benign

0.55

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