Variant 6-26016234-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 0.766 in 152,188 control chromosomes in the GnomAD database, including 45,443 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 0.77 ( 45442 hom., cov: 31)

Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 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:

0.766

AC:

116459

AN:

152068

Hom.:

45398

Cov.:

show subpopulations

Gnomad AFR

AF:

0.916

Gnomad AMI

AF:

0.651

Gnomad AMR

AF:

0.722

Gnomad ASJ

AF:

0.724

Gnomad EAS

AF:

0.865

Gnomad SAS

AF:

0.679

Gnomad FIN

AF:

0.711

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.694

Gnomad OTH

AF:

0.789

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.766

AC:

116559

AN:

152186

Hom.:

45442

Cov.:

AF XY:

0.766

AC XY:

56953

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.916

Gnomad4 AMR

AF:

0.722

Gnomad4 ASJ

AF:

0.724

Gnomad4 EAS

AF:

0.864

Gnomad4 SAS

AF:

0.679

Gnomad4 FIN

AF:

0.711

Gnomad4 NFE

AF:

0.694

Gnomad4 OTH

AF:

0.785

Alfa

AF:

0.703

Hom.:

51336

Bravo

AF:

0.776

Asia WGS

AF:

0.744

AC:

2590

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

DANN

Benign

0.85

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