Variant chr6-129710348-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 0.0774 in 486,954 control chromosomes in the GnomAD database, including 2,015 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 0.069 ( 539 hom., cov: 32)

Exomes 𝑓: 0.081 ( 1476 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.395

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 = 0.225 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:

0.0688

AC:

10469

AN:

152126

Hom.:

538

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0223

Gnomad AMI

AF:

0.0757

Gnomad AMR

AF:

0.0917

Gnomad ASJ

AF:

0.0738

Gnomad EAS

AF:

0.237

Gnomad SAS

AF:

0.122

Gnomad FIN

AF:

0.132

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0658

Gnomad OTH

AF:

0.0579

GnomAD4 exome

AF:

0.0813

AC:

27228

AN:

334710

Hom.:

1476

AF XY:

0.0821

AC XY:

14233

AN XY:

173438

show subpopulations

Gnomad4 AFR exome

AF:

0.0201

Gnomad4 AMR exome

AF:

0.0722

Gnomad4 ASJ exome

AF:

0.0712

Gnomad4 EAS exome

AF:

0.195

Gnomad4 SAS exome

AF:

0.105

Gnomad4 FIN exome

AF:

0.123

Gnomad4 NFE exome

AF:

0.0637

Gnomad4 OTH exome

AF:

0.0739

GnomAD4 genome

AF:

0.0687

AC:

10466

AN:

152244

Hom.:

539

Cov.:

AF XY:

0.0758

AC XY:

5639

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0222

Gnomad4 AMR

AF:

0.0917

Gnomad4 ASJ

AF:

0.0738

Gnomad4 EAS

AF:

0.236

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.132

Gnomad4 NFE

AF:

0.0658

Gnomad4 OTH

AF:

0.0601

Alfa

AF:

0.0625

Hom.:

306

Bravo

AF:

0.0622

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.0

DANN

Benign

0.65

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