Variant 1-16013965-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 0.615 in 152,120 control chromosomes in the GnomAD database, including 29,255 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 0.61 ( 29239 hom., cov: 32)

Exomes 𝑓: 0.55 ( 16 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.208

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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 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:

0.615

AC:

93388

AN:

151900

Hom.:

29220

Cov.:

show subpopulations

Gnomad AFR

AF:

0.704

Gnomad AMI

AF:

0.510

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.511

Gnomad EAS

AF:

0.774

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.556

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.592

Gnomad OTH

AF:

0.626

GnomAD4 exome

AF:

0.549

AC:

AN:

102

Hom.:

AF XY:

0.527

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.553

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.615

AC:

93447

AN:

152018

Hom.:

29239

Cov.:

AF XY:

0.609

AC XY:

45243

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.704

Gnomad4 AMR

AF:

0.492

Gnomad4 ASJ

AF:

0.511

Gnomad4 EAS

AF:

0.774

Gnomad4 SAS

AF:

0.596

Gnomad4 FIN

AF:

0.556

Gnomad4 NFE

AF:

0.592

Gnomad4 OTH

AF:

0.624

Alfa

AF:

0.598

Hom.:

12132

Bravo

AF:

0.611

Asia WGS

AF:

0.637

AC:

2216

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

Cadd

Benign

4.1

Dann

Benign

0.74

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