Variant 1-70439991-T-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 0.225 in 152,046 control chromosomes in the GnomAD database, including 4,840 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 0.23 ( 4838 hom., cov: 32)

Exomes 𝑓: 0.42 ( 2 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0680

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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.70439991T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.225

AC:

34223

AN:

151916

Hom.:

4841

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0538

Gnomad AMI

AF:

0.254

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.291

Gnomad EAS

AF:

0.220

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.272

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.230

GnomAD4 exome

AF:

0.417

AC:

AN:

Hom.:

AF XY:

0.417

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.225

AC:

34214

AN:

152034

Hom.:

4838

Cov.:

AF XY:

0.226

AC XY:

16783

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.0537

Gnomad4 AMR

AF:

0.336

Gnomad4 ASJ

AF:

0.291

Gnomad4 EAS

AF:

0.220

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.272

Gnomad4 NFE

AF:

0.293

Gnomad4 OTH

AF:

0.227

Alfa

AF:

0.276

Hom.:

9478

Bravo

AF:

0.227

Asia WGS

AF:

0.228

AC:

793

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.9

DANN

Benign

0.75

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