Variant chr15-82852284-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004839.4(HOMER2):c.652-32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 1,486,134 control chromosomes in the GnomAD database, including 462,003 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.82 ( 52004 hom., cov: 33)

Exomes 𝑓: 0.78 ( 409999 hom. )

Consequence

HOMER2
NM_004839.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00700

Variant links:

Genes affected

HOMER2 (HGNC:17513): (homer scaffold protein 2) This gene encodes a member of the homer family of dendritic proteins. Members of this family regulate group 1 metabotrophic glutamate receptor function. The encoded protein is a postsynaptic density scaffolding protein. Alternative splicing results in multiple transcript variants. Two related pseudogenes have been identified on chromosome 14. [provided by RefSeq, Jun 2011]

HOMER2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 15-82852284-C-T is Benign according to our data. Variant chr15-82852284-C-T is described in ClinVar as [Benign]. Clinvar id is 1267704.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HOMER2	NM_004839.4 linkuse as main transcript	c.652-32G>A		intron_variant		ENST00000450735.7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HOMER2	ENST00000450735.7 linkuse as main transcript	c.652-32G>A	intron_variant		1	NM_004839.4		Q9NSB8-2
HOMER2	ENST00000304231.12 linkuse as main transcript	c.685-32G>A	intron_variant		5		P1	Q9NSB8-1
HOMER2	ENST00000558817.1 linkuse as main transcript	c.409-32G>A	intron_variant		3
HOMER2	ENST00000558552.1 linkuse as main transcript	n.500G>A	non_coding_transcript_exon_variant	1/3	2

Frequencies

GnomAD3 genomes

AF:

0.824

AC:

125336

AN:

152142

Hom.:

51939

Cov.:

show subpopulations

Gnomad AFR

AF:

0.921

Gnomad AMI

AF:

0.664

Gnomad AMR

AF:

0.850

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.827

Gnomad SAS

AF:

0.654

Gnomad FIN

AF:

0.788

Gnomad MID

AF:

0.769

Gnomad NFE

AF:

0.782

Gnomad OTH

AF:

0.809

GnomAD3 exomes

AF:

0.795

AC:

193514

AN:

243430

Hom.:

77513

AF XY:

0.783

AC XY:

103516

AN XY:

132212

show subpopulations

Gnomad AFR exome

AF:

0.924

Gnomad AMR exome

AF:

0.897

Gnomad ASJ exome

AF:

0.761

Gnomad EAS exome

AF:

0.816

Gnomad SAS exome

AF:

0.663

Gnomad FIN exome

AF:

0.791

Gnomad NFE exome

AF:

0.783

Gnomad OTH exome

AF:

0.783

GnomAD4 exome

AF:

0.782

AC:

1043047

AN:

1333874

Hom.:

409999

Cov.:

AF XY:

0.777

AC XY:

520845

AN XY:

670376

show subpopulations

Gnomad4 AFR exome

AF:

0.927

Gnomad4 AMR exome

AF:

0.890

Gnomad4 ASJ exome

AF:

0.760

Gnomad4 EAS exome

AF:

0.842

Gnomad4 SAS exome

AF:

0.661

Gnomad4 FIN exome

AF:

0.791

Gnomad4 NFE exome

AF:

0.781

Gnomad4 OTH exome

AF:

0.776

GnomAD4 genome

AF:

0.824

AC:

125460

AN:

152260

Hom.:

52004

Cov.:

AF XY:

0.822

AC XY:

61152

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.921

Gnomad4 AMR

AF:

0.850

Gnomad4 ASJ

AF:

0.768

Gnomad4 EAS

AF:

0.828

Gnomad4 SAS

AF:

0.655

Gnomad4 FIN

AF:

0.788

Gnomad4 NFE

AF:

0.782

Gnomad4 OTH

AF:

0.809

Alfa

AF:

0.788

Hom.:

66666

Bravo

AF:

0.837

Asia WGS

AF:

0.775

AC:

2692

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.017

DANN

Benign

0.35

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over