Variant chr7-115035469-G-A 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 0.612 in 151,926 control chromosomes in the GnomAD database, including 28,598 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 0.61 ( 28598 hom., cov: 32)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.522

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 (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.115035469G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
LINC01393	ENST00000660905.1 linkuse as main transcript	n.244+3644G>A	intron_variant
LINC01393	ENST00000668211.1 linkuse as main transcript	n.137+3644G>A	intron_variant
LINC01393	ENST00000669990.1 linkuse as main transcript	n.160+3644G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.612

AC:

92941

AN:

151810

Hom.:

28582

Cov.:

show subpopulations

Gnomad AFR

AF:

0.562

Gnomad AMI

AF:

0.558

Gnomad AMR

AF:

0.582

Gnomad ASJ

AF:

0.646

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.602

Gnomad FIN

AF:

0.715

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.644

Gnomad OTH

AF:

0.603

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

GnomAD4 genome

AF:

0.612

AC:

93011

AN:

151926

Hom.:

28598

Cov.:

AF XY:

0.615

AC XY:

45655

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.562

Gnomad4 AMR

AF:

0.582

Gnomad4 ASJ

AF:

0.646

Gnomad4 EAS

AF:

0.480

Gnomad4 SAS

AF:

0.603

Gnomad4 FIN

AF:

0.715

Gnomad4 NFE

AF:

0.644

Gnomad4 OTH

AF:

0.604

Alfa

AF:

0.621

Hom.:

5002

Bravo

AF:

0.600

Asia WGS

AF:

0.572

AC:

1989

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.3

DANN

Benign

0.61

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