Variant 17-39667885-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 0.032 in 146,222 control chromosomes in the GnomAD database, including 113 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 0.032 ( 113 hom., cov: 25)

Exomes 𝑓: 0.0069 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.145

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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0503 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:

0.0321

AC:

4682

AN:

145966

Hom.:

113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0459

Gnomad AMR

AF:

0.0186

Gnomad ASJ

AF:

0.00645

Gnomad EAS

AF:

0.000667

Gnomad SAS

AF:

0.00379

Gnomad FIN

AF:

0.0396

Gnomad MID

AF:

0.0128

Gnomad NFE

AF:

0.0517

Gnomad OTH

AF:

0.0257

GnomAD4 exome

AF:

0.00694

AC:

AN:

144

Hom.:

AF XY:

0.00943

AC XY:

AN XY:

106

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00877

GnomAD4 genome

AF:

0.0321

AC:

4684

AN:

146078

Hom.:

113

Cov.:

AF XY:

0.0297

AC XY:

2119

AN XY:

71238

show subpopulations

Gnomad4 AFR

AF:

0.0118

Gnomad4 AMR

AF:

0.0186

Gnomad4 ASJ

AF:

0.00645

Gnomad4 EAS

AF:

0.000668

Gnomad4 SAS

AF:

0.00378

Gnomad4 FIN

AF:

0.0396

Gnomad4 NFE

AF:

0.0517

Gnomad4 OTH

AF:

0.0254

Alfa

AF:

0.0375

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.3

DANN

Benign

0.91

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