Variant X-141268958-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 0.29 in 110,726 control chromosomes in the GnomAD database, including 3,480 homozygotes. There are 9,184 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 0.29 ( 3480 hom., 9184 hem., cov: 23)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.525

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.141268958C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPANXA2-OT1	ENST00000662492.1 linkuse as main transcript	n.102+81121C>T		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

32138

AN:

110673

Hom.:

3481

Cov.:

AF XY:

0.278

AC XY:

9160

AN XY:

33007

show subpopulations

Gnomad AFR

AF:

0.312

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.249

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.291

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

GnomAD4 genome

AF:

0.290

AC:

32164

AN:

110726

Hom.:

3480

Cov.:

AF XY:

0.278

AC XY:

9184

AN XY:

33070

show subpopulations

Gnomad4 AFR

AF:

0.312

Gnomad4 AMR

AF:

0.270

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.126

Gnomad4 SAS

AF:

0.223

Gnomad4 FIN

AF:

0.321

Gnomad4 NFE

AF:

0.289

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.289

Hom.:

2169

Bravo

AF:

0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.76

DANN

Benign

0.53

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