Variant 10-121138399-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.488 in 152,080 control chromosomes in the GnomAD database, including 20,507 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.49 ( 20507 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.07

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.121138399G>A	intergenic_region
LOC124902515	XR_007062317.1 linkuse as main transcript	n.168-19050C>T	intron_variant
LOC124902515	XR_007062318.1 linkuse as main transcript	n.159-19050C>T	intron_variant
LOC105378522	XR_946379.3 linkuse as main transcript	n.356+8576G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.488

AC:

74205

AN:

151962

Hom.:

20508

Cov.:

show subpopulations

Gnomad AFR

AF:

0.231

Gnomad AMI

AF:

0.735

Gnomad AMR

AF:

0.459

Gnomad ASJ

AF:

0.634

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.759

Gnomad FIN

AF:

0.615

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.609

Gnomad OTH

AF:

0.516

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

GnomAD4 genome

AF:

0.488

AC:

74228

AN:

152080

Hom.:

20507

Cov.:

AF XY:

0.489

AC XY:

36364

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.231

Gnomad4 AMR

AF:

0.459

Gnomad4 ASJ

AF:

0.634

Gnomad4 EAS

AF:

0.378

Gnomad4 SAS

AF:

0.760

Gnomad4 FIN

AF:

0.615

Gnomad4 NFE

AF:

0.609

Gnomad4 OTH

AF:

0.516

Alfa

AF:

0.594

Hom.:

38853

Bravo

AF:

0.455

Asia WGS

AF:

0.531

AC:

1845

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Uncertain

-0.070

CADD

Benign

DANN

Benign

0.81

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