Variant rs11619306 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 0.386 in 151,954 control chromosomes in the GnomAD database, including 12,251 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 0.39 ( 12251 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 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:

0.386

AC:

58661

AN:

151836

Hom.:

12241

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.321

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.464

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.451

Gnomad OTH

AF:

0.391

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

GnomAD4 genome

AF:

0.386

AC:

58684

AN:

151954

Hom.:

12251

Cov.:

AF XY:

0.391

AC XY:

29018

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.497

Gnomad4 ASJ

AF:

0.409

Gnomad4 EAS

AF:

0.255

Gnomad4 SAS

AF:

0.414

Gnomad4 FIN

AF:

0.464

Gnomad4 NFE

AF:

0.451

Gnomad4 OTH

AF:

0.391

Alfa

AF:

0.419

Hom.:

1745

Bravo

AF:

0.381

Asia WGS

AF:

0.308

AC:

1071

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

8.0

DANN

Benign

0.43

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