Variant 2-37523837-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 0.595 in 151,882 control chromosomes in the GnomAD database, including 27,232 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 0.60 ( 27232 hom., cov: 31)

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0180

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 (AMR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.37523837A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect
ENSG00000287316	ENST00000668683.1 linkuse as main transcript	n.255-132A>G	intron_variant
LINC03063	ENST00000686061.1 linkuse as main transcript	n.122-13158A>G	intron_variant
LINC03063	ENST00000689279.1 linkuse as main transcript	n.122-13158A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.596

AC:

90387

AN:

151762

Hom.:

27214

Cov.:

show subpopulations

Gnomad AFR

AF:

0.548

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.639

Gnomad ASJ

AF:

0.547

Gnomad EAS

AF:

0.358

Gnomad SAS

AF:

0.476

Gnomad FIN

AF:

0.728

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.624

Gnomad OTH

AF:

0.585

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

GnomAD4 genome

AF:

0.595

AC:

90441

AN:

151882

Hom.:

27232

Cov.:

AF XY:

0.598

AC XY:

44369

AN XY:

74214

show subpopulations

Gnomad4 AFR

AF:

0.548

Gnomad4 AMR

AF:

0.639

Gnomad4 ASJ

AF:

0.547

Gnomad4 EAS

AF:

0.358

Gnomad4 SAS

AF:

0.477

Gnomad4 FIN

AF:

0.728

Gnomad4 NFE

AF:

0.624

Gnomad4 OTH

AF:

0.586

Alfa

AF:

0.601

Hom.:

39732

Bravo

AF:

0.589

Asia WGS

AF:

0.471

AC:

1636

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

6.3

DANN

Benign

0.64

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