Variant 6-29702484-A-G 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 0.248 in 152,102 control chromosomes in the GnomAD database, including 4,837 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 0.25 ( 4837 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.242

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 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:

0.248

AC:

37692

AN:

151984

Hom.:

4819

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.278

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.348

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.257

Gnomad OTH

AF:

0.246

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

GnomAD4 genome

AF:

0.248

AC:

37733

AN:

152102

Hom.:

4837

Cov.:

AF XY:

0.244

AC XY:

18157

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.230

Gnomad4 AMR

AF:

0.279

Gnomad4 ASJ

AF:

0.182

Gnomad4 EAS

AF:

0.348

Gnomad4 SAS

AF:

0.335

Gnomad4 FIN

AF:

0.148

Gnomad4 NFE

AF:

0.257

Gnomad4 OTH

AF:

0.252

Alfa

AF:

0.257

Hom.:

8005

Bravo

AF:

0.255

Asia WGS

AF:

0.414

AC:

1442

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

5.1

DANN

Benign

0.44

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