Variant X-137515426-C-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 0.344 in 110,479 control chromosomes in the GnomAD database, including 5,131 homozygotes. There are 10,551 hemizygotes in GnomAD. 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 0.34 ( 5131 hom., 10551 hem., cov: 22)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.243

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.137515426C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

37953

AN:

110426

Hom.:

5131

Cov.:

AF XY:

0.322

AC XY:

10540

AN XY:

32710

show subpopulations

Gnomad AFR

AF:

0.480

Gnomad AMI

AF:

0.320

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.343

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.233

Gnomad MID

AF:

0.364

Gnomad NFE

AF:

0.302

Gnomad OTH

AF:

0.319

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

GnomAD4 genome

AF:

0.344

AC:

37960

AN:

110479

Hom.:

5131

Cov.:

AF XY:

0.322

AC XY:

10551

AN XY:

32773

show subpopulations

Gnomad4 AFR

AF:

0.480

Gnomad4 AMR

AF:

0.251

Gnomad4 ASJ

AF:

0.335

Gnomad4 EAS

AF:

0.343

Gnomad4 SAS

AF:

0.245

Gnomad4 FIN

AF:

0.233

Gnomad4 NFE

AF:

0.302

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.326

Hom.:

2296

Bravo

AF:

0.351

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.5

DANN

Benign

0.78

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