Variant 18-13916295-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 0.355 in 152,068 control chromosomes in the GnomAD database, including 10,563 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 0.36 ( 10563 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.161

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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 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:

0.355

AC:

53997

AN:

151950

Hom.:

10565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.345

Gnomad AMR

AF:

0.342

Gnomad ASJ

AF:

0.437

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.504

Gnomad MID

AF:

0.525

Gnomad NFE

AF:

0.438

Gnomad OTH

AF:

0.376

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

GnomAD4 genome

AF:

0.355

AC:

54008

AN:

152068

Hom.:

10563

Cov.:

AF XY:

0.356

AC XY:

26414

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.342

Gnomad4 ASJ

AF:

0.437

Gnomad4 EAS

AF:

0.214

Gnomad4 SAS

AF:

0.236

Gnomad4 FIN

AF:

0.504

Gnomad4 NFE

AF:

0.438

Gnomad4 OTH

AF:

0.370

Alfa

AF:

0.393

Hom.:

1537

Bravo

AF:

0.339

Asia WGS

AF:

0.232

AC:

809

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.0

DANN

Benign

0.72

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