Variant rs1081105 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The variant allele was found at a frequency of 0.0282 in 195,214 control chromosomes in the GnomAD database, including 89 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 0.029 ( 65 hom., cov: 32)

Exomes 𝑓: 0.024 ( 24 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.849

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=-0.92).

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0294 (4450/151368) while in subpopulation AFR AF= 0.0479 (1975/41258). AF 95% confidence interval is 0.0461. There are 65 homozygotes in gnomad4. There are 2157 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 65 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0294

AC:

4447

AN:

151250

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0479

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0138

Gnomad ASJ

AF:

0.0310

Gnomad EAS

AF:

0.00237

Gnomad SAS

AF:

0.0263

Gnomad FIN

AF:

0.0206

Gnomad MID

AF:

0.0227

Gnomad NFE

AF:

0.0259

Gnomad OTH

AF:

0.0216

GnomAD4 exome

AF:

0.0242

AC:

1063

AN:

43846

Hom.:

Cov.:

AF XY:

0.0230

AC XY:

533

AN XY:

23218

show subpopulations

Gnomad4 AFR exome

AF:

0.0599

Gnomad4 AMR exome

AF:

0.0159

Gnomad4 ASJ exome

AF:

0.0346

Gnomad4 EAS exome

AF:

0.00111

Gnomad4 SAS exome

AF:

0.0192

Gnomad4 FIN exome

AF:

0.0213

Gnomad4 NFE exome

AF:

0.0269

Gnomad4 OTH exome

AF:

0.0253

GnomAD4 genome

AF:

0.0294

AC:

4450

AN:

151368

Hom.:

Cov.:

AF XY:

0.0292

AC XY:

2157

AN XY:

73972

show subpopulations

Gnomad4 AFR

AF:

0.0479

Gnomad4 AMR

AF:

0.0137

Gnomad4 ASJ

AF:

0.0310

Gnomad4 EAS

AF:

0.00237

Gnomad4 SAS

AF:

0.0261

Gnomad4 FIN

AF:

0.0206

Gnomad4 NFE

AF:

0.0259

Gnomad4 OTH

AF:

0.0214

Alfa

AF:

0.153

Hom.:

1409

Bravo

AF:

0.0299

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.2

DANN

Benign

0.44

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