Variant rs11704319 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 0.305 in 151,510 control chromosomes in the GnomAD database, including 8,304 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 ( 8304 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28

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 (EAS) allele frequency at 95% confidence interval = 0.788 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:

0.305

AC:

46107

AN:

151396

Hom.:

8295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.364

Gnomad ASJ

AF:

0.275

Gnomad EAS

AF:

0.809

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.384

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.319

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

GnomAD4 genome

AF:

0.305

AC:

46141

AN:

151510

Hom.:

8304

Cov.:

AF XY:

0.314

AC XY:

23275

AN XY:

74034

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.364

Gnomad4 ASJ

AF:

0.275

Gnomad4 EAS

AF:

0.809

Gnomad4 SAS

AF:

0.416

Gnomad4 FIN

AF:

0.384

Gnomad4 NFE

AF:

0.310

Gnomad4 OTH

AF:

0.323

Alfa

AF:

0.308

Hom.:

5611

Bravo

AF:

0.302

Asia WGS

AF:

0.567

AC:

1966

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

DANN

Benign

0.59

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