rs1010820

chr15-82946202-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004839.4(HOMER2):c.5+6329A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,164 control chromosomes in the GnomAD database, including 3,027 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 0.19 (3027 hom., cov: 32)
• Consequence: HOMER2 NM_004839.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HOMER2	NM_004839.4	c.5+6329A>T		intron_variant		ENST00000450735.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HOMER2	ENST00000450735.7	c.5+6329A>T		intron_variant		1	NM_004839.4
	ENST00000566841.1	n.734+19585T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29365 AN: 152046 Hom.: 3026 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.00442

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.193 AC: 29387 AN: 152164 Hom.: 3027 Cov.: 32 AF XY: 0.187 AC XY: 13906 AN XY: 74378

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.00444

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.186

Alfa AF: 0.210 Hom.: 407

Bravo AF: 0.196

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.74
Dann	Benign	0.46

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

Other links and lift over

dbSNP: rs1010820; hg19: chr15-83614954;