Variant chr6-154009670-T-A 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 0.487 in 151,856 control chromosomes in the GnomAD database, including 18,406 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 ( 18406 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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:

0.487

AC:

73960

AN:

151738

Hom.:

18396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.403

Gnomad AMI

AF:

0.562

Gnomad AMR

AF:

0.589

Gnomad ASJ

AF:

0.553

Gnomad EAS

AF:

0.730

Gnomad SAS

AF:

0.597

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.478

Gnomad OTH

AF:

0.499

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

GnomAD4 genome

AF:

0.487

AC:

74009

AN:

151856

Hom.:

18406

Cov.:

AF XY:

0.497

AC XY:

36841

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.403

Gnomad4 AMR

AF:

0.590

Gnomad4 ASJ

AF:

0.553

Gnomad4 EAS

AF:

0.729

Gnomad4 SAS

AF:

0.596

Gnomad4 FIN

AF:

0.537

Gnomad4 NFE

AF:

0.478

Gnomad4 OTH

AF:

0.501

Alfa

AF:

0.357

Hom.:

976

Bravo

AF:

0.484

Asia WGS

AF:

0.675

AC:

2346

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.26

DANN

Benign

0.46

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