Variant 12-97245366-A-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 0.669 in 517,280 control chromosomes in the GnomAD database, including 118,212 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 0.64 ( 32297 hom., cov: 32)

Exomes 𝑓: 0.68 ( 85915 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.801

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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.97245366A>G	intergenic_region
LOC101928912	XR_246024.4 linkuse as main transcript	n.223+7402T>C	intron_variant
LOC101928912	XR_945251.3 linkuse as main transcript	n.224-1644T>C	intron_variant
LOC101928912	XR_945252.3 linkuse as main transcript	n.224-4304T>C	intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.643

AC:

97551

AN:

151756

Hom.:

32292

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.835

Gnomad AMR

AF:

0.671

Gnomad ASJ

AF:

0.788

Gnomad EAS

AF:

0.669

Gnomad SAS

AF:

0.551

Gnomad FIN

AF:

0.676

Gnomad MID

AF:

0.763

Gnomad NFE

AF:

0.722

Gnomad OTH

AF:

0.692

GnomAD3 exomes

AF:

0.677

AC:

154159

AN:

227740

Hom.:

53097

AF XY:

0.677

AC XY:

85206

AN XY:

125942

show subpopulations

Gnomad AFR exome

AF:

0.473

Gnomad AMR exome

AF:

0.668

Gnomad ASJ exome

AF:

0.793

Gnomad EAS exome

AF:

0.672

Gnomad SAS exome

AF:

0.551

Gnomad FIN exome

AF:

0.685

Gnomad NFE exome

AF:

0.730

Gnomad OTH exome

AF:

0.707

GnomAD4 exome

AF:

0.680

AC:

248546

AN:

365406

Hom.:

85915

Cov.:

AF XY:

0.671

AC XY:

140734

AN XY:

209604

show subpopulations

Gnomad4 AFR exome

AF:

0.474

Gnomad4 AMR exome

AF:

0.669

Gnomad4 ASJ exome

AF:

0.798

Gnomad4 EAS exome

AF:

0.678

Gnomad4 SAS exome

AF:

0.556

Gnomad4 FIN exome

AF:

0.694

Gnomad4 NFE exome

AF:

0.726

Gnomad4 OTH exome

AF:

0.705

GnomAD4 genome

AF:

0.643

AC:

97601

AN:

151874

Hom.:

32297

Cov.:

AF XY:

0.641

AC XY:

47597

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.481

Gnomad4 AMR

AF:

0.671

Gnomad4 ASJ

AF:

0.788

Gnomad4 EAS

AF:

0.669

Gnomad4 SAS

AF:

0.551

Gnomad4 FIN

AF:

0.676

Gnomad4 NFE

AF:

0.722

Gnomad4 OTH

AF:

0.690

Alfa

AF:

0.719

Hom.:

92959

Bravo

AF:

0.641

Asia WGS

AF:

0.566

AC:

1967

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

DANN

Benign

0.65

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