Variant rs1370072 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 0.34 in 151,920 control chromosomes in the GnomAD database, including 10,549 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 0.34 ( 10549 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

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=-0.74).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 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:

0.341

AC:

51721

AN:

151802

Hom.:

10551

Cov.:

show subpopulations

Gnomad AFR

AF:

0.121

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.375

Gnomad ASJ

AF:

0.412

Gnomad EAS

AF:

0.265

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.521

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.446

Gnomad OTH

AF:

0.353

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

GnomAD4 genome

AF:

0.340

AC:

51718

AN:

151920

Hom.:

10549

Cov.:

AF XY:

0.342

AC XY:

25382

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.121

Gnomad4 AMR

AF:

0.375

Gnomad4 ASJ

AF:

0.412

Gnomad4 EAS

AF:

0.265

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.521

Gnomad4 NFE

AF:

0.446

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.411

Hom.:

9731

Bravo

AF:

0.322

Asia WGS

AF:

0.246

AC:

855

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.63

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