Variant 2-218145423-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 0.521 in 151,982 control chromosomes in the GnomAD database, including 21,162 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 0.52 ( 21162 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.19

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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.218145423C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.521

AC:

79105

AN:

151864

Hom.:

21138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.624

Gnomad AMI

AF:

0.688

Gnomad AMR

AF:

0.518

Gnomad ASJ

AF:

0.574

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.492

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.658

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.547

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

GnomAD4 genome

AF:

0.521

AC:

79151

AN:

151982

Hom.:

21162

Cov.:

AF XY:

0.515

AC XY:

38294

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.624

Gnomad4 AMR

AF:

0.517

Gnomad4 ASJ

AF:

0.574

Gnomad4 EAS

AF:

0.329

Gnomad4 SAS

AF:

0.492

Gnomad4 FIN

AF:

0.400

Gnomad4 NFE

AF:

0.488

Gnomad4 OTH

AF:

0.546

Alfa

AF:

0.497

Hom.:

42533

Bravo

AF:

0.533

Asia WGS

AF:

0.394

AC:

1370

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.14

DANN

Benign

0.73

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