Variant chr6-88137716-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 0.497 in 152,078 control chromosomes in the GnomAD database, including 19,616 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 0.50 ( 19616 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.123

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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 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:

0.497

AC:

75581

AN:

151960

Hom.:

19624

Cov.:

show subpopulations

Gnomad AFR

AF:

0.512

Gnomad AMI

AF:

0.431

Gnomad AMR

AF:

0.371

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.0876

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.604

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.544

Gnomad OTH

AF:

0.464

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

GnomAD4 genome

AF:

0.497

AC:

75595

AN:

152078

Hom.:

19616

Cov.:

AF XY:

0.492

AC XY:

36599

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.511

Gnomad4 AMR

AF:

0.371

Gnomad4 ASJ

AF:

0.424

Gnomad4 EAS

AF:

0.0874

Gnomad4 SAS

AF:

0.409

Gnomad4 FIN

AF:

0.604

Gnomad4 NFE

AF:

0.544

Gnomad4 OTH

AF:

0.462

Alfa

AF:

0.519

Hom.:

11837

Bravo

AF:

0.479

Asia WGS

AF:

0.285

AC:

990

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

7.3

DANN

Benign

0.81

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