Variant chr7-150984122-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 0.303 in 152,120 control chromosomes in the GnomAD database, including 7,641 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 0.30 ( 7641 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0140

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=-0.68).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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:

0.303

AC:

46129

AN:

152004

Hom.:

7639

Cov.:

show subpopulations

Gnomad AFR

AF:

0.195

Gnomad AMI

AF:

0.453

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.304

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.291

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

GnomAD4 genome

AF:

0.303

AC:

46144

AN:

152120

Hom.:

7641

Cov.:

AF XY:

0.300

AC XY:

22295

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.195

Gnomad4 AMR

AF:

0.291

Gnomad4 ASJ

AF:

0.318

Gnomad4 EAS

AF:

0.135

Gnomad4 SAS

AF:

0.304

Gnomad4 FIN

AF:

0.353

Gnomad4 NFE

AF:

0.376

Gnomad4 OTH

AF:

0.285

Alfa

AF:

0.357

Hom.:

15703

Bravo

AF:

0.294

Asia WGS

AF:

0.223

AC:

778

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

9.2

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