Variant X-143075435-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 0.311 in 110,307 control chromosomes in the GnomAD database, including 4,470 homozygotes. There are 9,708 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 0.31 ( 4470 hom., 9708 hem., cov: 22)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.504

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.143075435C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

34282

AN:

110258

Hom.:

4465

Cov.:

AF XY:

0.297

AC XY:

9675

AN XY:

32532

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.244

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.280

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.196

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.349

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

GnomAD4 genome

AF:

0.311

AC:

34325

AN:

110307

Hom.:

4470

Cov.:

AF XY:

0.298

AC XY:

9708

AN XY:

32591

show subpopulations

Gnomad4 AFR

AF:

0.501

Gnomad4 AMR

AF:

0.367

Gnomad4 ASJ

AF:

0.280

Gnomad4 EAS

AF:

0.348

Gnomad4 SAS

AF:

0.196

Gnomad4 FIN

AF:

0.193

Gnomad4 NFE

AF:

0.209

Gnomad4 OTH

AF:

0.346

Alfa

AF:

0.220

Hom.:

17227

Bravo

AF:

0.342

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.1

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