Variant rs1376178 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 0.485 in 151,978 control chromosomes in the GnomAD database, including 19,106 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 0.48 ( 19106 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.175

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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:

0.484

AC:

73570

AN:

151860

Hom.:

19075

Cov.:

show subpopulations

Gnomad AFR

AF:

0.693

Gnomad AMI

AF:

0.473

Gnomad AMR

AF:

0.450

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.542

Gnomad SAS

AF:

0.451

Gnomad FIN

AF:

0.372

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.463

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

GnomAD4 genome

AF:

0.485

AC:

73661

AN:

151978

Hom.:

19106

Cov.:

AF XY:

0.482

AC XY:

35824

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.693

Gnomad4 AMR

AF:

0.449

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.541

Gnomad4 SAS

AF:

0.453

Gnomad4 FIN

AF:

0.372

Gnomad4 NFE

AF:

0.390

Gnomad4 OTH

AF:

0.460

Alfa

AF:

0.407

Hom.:

21723

Bravo

AF:

0.502

Asia WGS

AF:

0.524

AC:

1823

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.6

DANN

Benign

0.31

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