Variant 5-79450876-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004272.5(HOMER1):c.294+114G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,041,592 control chromosomes in the GnomAD database, including 39,023 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 0.26 ( 5366 hom., cov: 32)

Exomes 𝑓: 0.27 ( 33657 hom. )

Consequence

HOMER1
NM_004272.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.780

Variant links:

Genes affected

HOMER1 (HGNC:17512): (homer scaffold protein 1) This gene encodes a member of the homer family of dendritic proteins. Members of this family regulate group 1 metabotrophic glutamate receptor function. [provided by RefSeq, Jul 2008]

HOMER1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HOMER1	NM_004272.5 linkuse as main transcript	c.294+114G>A		intron_variant		ENST00000334082.11

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
HOMER1	ENST00000334082.11 linkuse as main transcript	c.294+114G>A	intron_variant	1	NM_004272.5	P1	Q86YM7-1
HOMER1	ENST00000282260.10 linkuse as main transcript	c.294+114G>A	intron_variant	1			Q86YM7-2
HOMER1	ENST00000508576.5 linkuse as main transcript	c.294+114G>A	intron_variant	1			Q86YM7-3
HOMER1	ENST00000535690.1 linkuse as main transcript	c.6-48821G>A	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39902

AN:

151908

Hom.:

5356

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.208

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.283

GnomAD4 exome

AF:

0.271

AC:

240840

AN:

889566

Hom.:

33657

AF XY:

0.274

AC XY:

121421

AN XY:

442946

show subpopulations

Gnomad4 AFR exome

AF:

0.264

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.362

Gnomad4 EAS exome

AF:

0.163

Gnomad4 SAS exome

AF:

0.373

Gnomad4 FIN exome

AF:

0.218

Gnomad4 NFE exome

AF:

0.270

Gnomad4 OTH exome

AF:

0.274

GnomAD4 genome

AF:

0.263

AC:

39942

AN:

152026

Hom.:

5366

Cov.:

AF XY:

0.264

AC XY:

19609

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.261

Gnomad4 AMR

AF:

0.255

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.145

Gnomad4 SAS

AF:

0.372

Gnomad4 FIN

AF:

0.208

Gnomad4 NFE

AF:

0.272

Gnomad4 OTH

AF:

0.287

Alfa

AF:

0.159

Hom.:

292

Bravo

AF:

0.260

Asia WGS

AF:

0.296

AC:

1032

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.1

DANN

Benign

0.77

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over