Variant 2-65055574-G-C 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 0.286 in 152,052 control chromosomes in the GnomAD database, including 6,492 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 0.29 ( 6492 hom., cov: 33)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

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 (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.65055574G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
LINC02245	ENST00000653778.1 linkuse as main transcript	n.254+341C>G	intron_variant
LINC02245	ENST00000666526.2 linkuse as main transcript	n.312+341C>G	intron_variant
LINC02245	ENST00000685506.2 linkuse as main transcript	n.291+341C>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.286

AC:

43457

AN:

151934

Hom.:

6470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.272

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.325

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.212

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.302

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

GnomAD4 genome

AF:

0.286

AC:

43524

AN:

152052

Hom.:

6492

Cov.:

AF XY:

0.284

AC XY:

21083

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.349

Gnomad4 AMR

AF:

0.272

Gnomad4 ASJ

AF:

0.387

Gnomad4 EAS

AF:

0.324

Gnomad4 SAS

AF:

0.310

Gnomad4 FIN

AF:

0.212

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.310

Alfa

AF:

0.281

Hom.:

775

Bravo

AF:

0.293

Asia WGS

AF:

0.387

AC:

1347

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

9.2

DANN

Benign

0.70

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