Variant chr16-3241970-C-A 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 0.592 in 152,858 control chromosomes in the GnomAD database, including 27,082 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 0.59 ( 26899 hom., cov: 33)

Exomes 𝑓: 0.67 ( 183 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0370

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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.707 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:

0.591

AC:

89821

AN:

151920

Hom.:

26858

Cov.:

show subpopulations

Gnomad AFR

AF:

0.662

Gnomad AMI

AF:

0.402

Gnomad AMR

AF:

0.625

Gnomad ASJ

AF:

0.564

Gnomad EAS

AF:

0.614

Gnomad SAS

AF:

0.729

Gnomad FIN

AF:

0.559

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.539

Gnomad OTH

AF:

0.576

GnomAD4 exome

AF:

0.670

AC:

549

AN:

820

Hom.:

183

AF XY:

0.694

AC XY:

412

AN XY:

594

show subpopulations

Gnomad4 AMR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.375

Gnomad4 EAS exome

AF:

0.500

Gnomad4 SAS exome

AF:

0.711

Gnomad4 FIN exome

AF:

0.639

Gnomad4 NFE exome

AF:

0.607

Gnomad4 OTH exome

AF:

0.625

GnomAD4 genome

AF:

0.591

AC:

89922

AN:

152038

Hom.:

26899

Cov.:

AF XY:

0.596

AC XY:

44265

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.662

Gnomad4 AMR

AF:

0.625

Gnomad4 ASJ

AF:

0.564

Gnomad4 EAS

AF:

0.614

Gnomad4 SAS

AF:

0.727

Gnomad4 FIN

AF:

0.559

Gnomad4 NFE

AF:

0.539

Gnomad4 OTH

AF:

0.577

Alfa

AF:

0.553

Hom.:

30900

Bravo

AF:

0.599

Asia WGS

AF:

0.692

AC:

2406

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.52

DANN

Benign

0.39

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