Variant rs1895858 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 0.248 in 152,214 control chromosomes in the GnomAD database, including 5,082 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 0.25 ( 5082 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.253

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=-0.67).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.305 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:

0.249

AC:

37820

AN:

152096

Hom.:

5083

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.304

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.217

Gnomad SAS

AF:

0.260

Gnomad FIN

AF:

0.202

Gnomad MID

AF:

0.299

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.236

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

GnomAD4 genome

AF:

0.248

AC:

37813

AN:

152214

Hom.:

5082

Cov.:

AF XY:

0.243

AC XY:

18117

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.216

Gnomad4 SAS

AF:

0.259

Gnomad4 FIN

AF:

0.202

Gnomad4 NFE

AF:

0.309

Gnomad4 OTH

AF:

0.234

Alfa

AF:

0.292

Hom.:

3041

Bravo

AF:

0.243

Asia WGS

AF:

0.234

AC:

812

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

8.6

DANN

Benign

0.62

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