Variant 18-10078074-G-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 0.226 in 152,148 control chromosomes in the GnomAD database, including 4,112 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 0.23 ( 4112 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 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:

0.226

AC:

34334

AN:

152030

Hom.:

4113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.179

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.236

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

GnomAD4 genome

AF:

0.226

AC:

34344

AN:

152148

Hom.:

4112

Cov.:

AF XY:

0.225

AC XY:

16719

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.251

Gnomad4 ASJ

AF:

0.232

Gnomad4 EAS

AF:

0.287

Gnomad4 SAS

AF:

0.179

Gnomad4 FIN

AF:

0.245

Gnomad4 NFE

AF:

0.268

Gnomad4 OTH

AF:

0.235

Alfa

AF:

0.259

Hom.:

5659

Bravo

AF:

0.225

Asia WGS

AF:

0.223

AC:

775

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.30

DANN

Benign

0.40

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