Variant 1-217353682-C-G 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 0.665 in 151,844 control chromosomes in the GnomAD database, including 35,788 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 0.66 ( 35788 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.221

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.217353682C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.665

AC:

100863

AN:

151726

Hom.:

35778

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.711

Gnomad AMR

AF:

0.724

Gnomad ASJ

AF:

0.749

Gnomad EAS

AF:

0.822

Gnomad SAS

AF:

0.675

Gnomad FIN

AF:

0.840

Gnomad MID

AF:

0.650

Gnomad NFE

AF:

0.770

Gnomad OTH

AF:

0.670

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

GnomAD4 genome

AF:

0.665

AC:

100902

AN:

151844

Hom.:

35788

Cov.:

AF XY:

0.668

AC XY:

49586

AN XY:

74196

show subpopulations

Gnomad4 AFR

AF:

0.396

Gnomad4 AMR

AF:

0.724

Gnomad4 ASJ

AF:

0.749

Gnomad4 EAS

AF:

0.823

Gnomad4 SAS

AF:

0.675

Gnomad4 FIN

AF:

0.840

Gnomad4 NFE

AF:

0.770

Gnomad4 OTH

AF:

0.668

Alfa

AF:

0.748

Hom.:

21463

Bravo

AF:

0.647

Asia WGS

AF:

0.703

AC:

2445

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

4.0

DANN

Benign

0.69

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