Variant 10-45374099-TGCGGGGGCGGGGGCGGGGGCGGGG-TGCGGGGGCGGGG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.0263 in 821,896 control chromosomes in the GnomAD database, including 3,443 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 2469 hom., cov: 22)

Exomes 𝑓: 0.0099 ( 974 hom. )

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.984

Variant links:

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ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

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:

0.0995

AC:

14902

AN:

149838

Hom.:

2464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0399

Gnomad ASJ

AF:

0.00203

Gnomad EAS

AF:

0.000826

Gnomad SAS

AF:

0.00425

Gnomad FIN

AF:

0.0000969

Gnomad MID

AF:

0.0194

Gnomad NFE

AF:

0.00190

Gnomad OTH

AF:

0.0786

GnomAD4 exome

AF:

0.00992

AC:

6668

AN:

671956

Hom.:

974

AF XY:

0.00908

AC XY:

2955

AN XY:

325606

show subpopulations

Gnomad4 AFR exome

AF:

0.355

Gnomad4 AMR exome

AF:

0.0285

Gnomad4 ASJ exome

AF:

0.00224

Gnomad4 EAS exome

AF:

0.00182

Gnomad4 SAS exome

AF:

0.00652

Gnomad4 FIN exome

AF:

0.0000967

Gnomad4 NFE exome

AF:

0.00144

Gnomad4 OTH exome

AF:

0.0264

GnomAD4 genome

AF:

0.0996

AC:

14940

AN:

149940

Hom.:

2469

Cov.:

AF XY:

0.0948

AC XY:

6928

AN XY:

73116

show subpopulations

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.0399

Gnomad4 ASJ

AF:

0.00203

Gnomad4 EAS

AF:

0.000829

Gnomad4 SAS

AF:

0.00404

Gnomad4 FIN

AF:

0.0000969

Gnomad4 NFE

AF:

0.00190

Gnomad4 OTH

AF:

0.0811

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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