Variant 17-65307301-C-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 0.292 in 152,120 control chromosomes in the GnomAD database, including 7,215 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 0.29 ( 7215 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

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=-0.58).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 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:

0.291

AC:

44292

AN:

152002

Hom.:

7199

Cov.:

show subpopulations

Gnomad AFR

AF:

0.415

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.0291

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.299

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

GnomAD4 genome

AF:

0.292

AC:

44356

AN:

152120

Hom.:

7215

Cov.:

AF XY:

0.285

AC XY:

21174

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.415

Gnomad4 AMR

AF:

0.223

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.0291

Gnomad4 SAS

AF:

0.181

Gnomad4 FIN

AF:

0.254

Gnomad4 NFE

AF:

0.268

Gnomad4 OTH

AF:

0.299

Alfa

AF:

0.306

Hom.:

1341

Bravo

AF:

0.296

Asia WGS

AF:

0.131

AC:

457

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.68

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