Variant 1-185461362-G-T 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 0.333 in 151,376 control chromosomes in the GnomAD database, including 9,498 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 0.33 ( 9498 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.316

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 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:

0.333

AC:

50371

AN:

151280

Hom.:

9482

Cov.:

show subpopulations

Gnomad AFR

AF:

0.500

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.216

Gnomad EAS

AF:

0.575

Gnomad SAS

AF:

0.227

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.338

Gnomad NFE

AF:

0.241

Gnomad OTH

AF:

0.309

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

GnomAD4 genome

AF:

0.333

AC:

50427

AN:

151376

Hom.:

9498

Cov.:

AF XY:

0.334

AC XY:

24660

AN XY:

73872

show subpopulations

Gnomad4 AFR

AF:

0.500

Gnomad4 AMR

AF:

0.322

Gnomad4 ASJ

AF:

0.216

Gnomad4 EAS

AF:

0.576

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.241

Gnomad4 OTH

AF:

0.308

Alfa

AF:

0.260

Hom.:

5274

Bravo

AF:

0.347

Asia WGS

AF:

0.437

AC:

1519

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.62

DANN

Benign

0.29

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