Variant 10-43678196-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 0.388 in 151,732 control chromosomes in the GnomAD database, including 11,589 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 0.39 ( 11589 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.230

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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.437 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:

0.387

AC:

58726

AN:

151614

Hom.:

11565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.442

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.398

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.389

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.376

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

GnomAD4 genome

AF:

0.388

AC:

58797

AN:

151732

Hom.:

11589

Cov.:

AF XY:

0.385

AC XY:

28519

AN XY:

74152

show subpopulations

Gnomad4 AFR

AF:

0.442

Gnomad4 AMR

AF:

0.399

Gnomad4 ASJ

AF:

0.311

Gnomad4 EAS

AF:

0.285

Gnomad4 SAS

AF:

0.388

Gnomad4 FIN

AF:

0.345

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.280

Hom.:

907

Bravo

AF:

0.394

Asia WGS

AF:

0.379

AC:

1317

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.79

DANN

Benign

0.57

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