Variant rs1468326 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 0.794 in 150,748 control chromosomes in the GnomAD database, including 48,263 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 0.79 ( 48263 hom., cov: 25)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.301

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.878 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:

0.794

AC:

119658

AN:

150630

Hom.:

48252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.654

Gnomad AMI

AF:

0.907

Gnomad AMR

AF:

0.820

Gnomad ASJ

AF:

0.814

Gnomad EAS

AF:

0.633

Gnomad SAS

AF:

0.820

Gnomad FIN

AF:

0.777

Gnomad MID

AF:

0.826

Gnomad NFE

AF:

0.884

Gnomad OTH

AF:

0.800

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

GnomAD4 genome

AF:

0.794

AC:

119706

AN:

150748

Hom.:

48263

Cov.:

AF XY:

0.791

AC XY:

58208

AN XY:

73594

show subpopulations

Gnomad4 AFR

AF:

0.653

Gnomad4 AMR

AF:

0.820

Gnomad4 ASJ

AF:

0.814

Gnomad4 EAS

AF:

0.633

Gnomad4 SAS

AF:

0.820

Gnomad4 FIN

AF:

0.777

Gnomad4 NFE

AF:

0.884

Gnomad4 OTH

AF:

0.795

Alfa

AF:

0.865

Hom.:

49084

Bravo

AF:

0.791

Asia WGS

AF:

0.713

AC:

2481

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.4

DANN

Benign

0.76

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