Variant rs1373494 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 0.203 in 152,138 control chromosomes in the GnomAD database, including 4,555 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 0.20 ( 4555 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0110

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 (AFR) allele frequency at 95% confidence interval = 0.394 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:

0.202

AC:

30771

AN:

152020

Hom.:

4543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.0373

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.320

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.139

Gnomad NFE

AF:

0.0953

Gnomad OTH

AF:

0.182

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

GnomAD4 genome

AF:

0.203

AC:

30815

AN:

152138

Hom.:

4555

Cov.:

AF XY:

0.205

AC XY:

15277

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.399

Gnomad4 AMR

AF:

0.211

Gnomad4 ASJ

AF:

0.138

Gnomad4 EAS

AF:

0.319

Gnomad4 SAS

AF:

0.156

Gnomad4 FIN

AF:

0.115

Gnomad4 NFE

AF:

0.0954

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.181

Hom.:

682

Bravo

AF:

0.216

Asia WGS

AF:

0.289

AC:

1005

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

2.2

DANN

Benign

0.38

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