Variant 10-44768973-A-G 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 0.317 in 152,100 control chromosomes in the GnomAD database, including 8,012 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 0.32 ( 8012 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.115

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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 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:

0.317

AC:

48229

AN:

151980

Hom.:

7991

Cov.:

show subpopulations

Gnomad AFR

AF:

0.434

Gnomad AMI

AF:

0.358

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.261

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.310

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.314

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

GnomAD4 genome

AF:

0.317

AC:

48283

AN:

152100

Hom.:

8012

Cov.:

AF XY:

0.316

AC XY:

23496

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.434

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.335

Gnomad4 EAS

AF:

0.260

Gnomad4 SAS

AF:

0.192

Gnomad4 FIN

AF:

0.310

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.281

Hom.:

7814

Bravo

AF:

0.319

Asia WGS

AF:

0.235

AC:

815

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.9

DANN

Benign

0.35

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