Variant chr17-32912627-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 0.211 in 152,130 control chromosomes in the GnomAD database, including 3,597 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 0.21 ( 3597 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

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=-0.7).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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:

0.211

AC:

32022

AN:

152012

Hom.:

3589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.213

Gnomad AMR

AF:

0.204

Gnomad ASJ

AF:

0.272

Gnomad EAS

AF:

0.00635

Gnomad SAS

AF:

0.207

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.226

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

GnomAD4 genome

AF:

0.211

AC:

32060

AN:

152130

Hom.:

3597

Cov.:

AF XY:

0.206

AC XY:

15332

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.266

Gnomad4 AMR

AF:

0.204

Gnomad4 ASJ

AF:

0.272

Gnomad4 EAS

AF:

0.00636

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.170

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.200

Hom.:

5285

Bravo

AF:

0.214

Asia WGS

AF:

0.125

AC:

432

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

9.2

DANN

Benign

0.81

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