5-79460955-T-C

Position:

• chr5-79460955-T-C

Variant summary

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

The NM_004272.5(HOMER1):​c.6-3937A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,922 control chromosomes in the GnomAD database, including 3,661 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 0.22 (3661 hom., cov: 32)
• Consequence: HOMER1 NM_004272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HOMER1	NM_004272.5	c.6-3937A>G		intron_variant		ENST00000334082.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HOMER1	ENST00000334082.11	c.6-3937A>G		intron_variant		1	NM_004272.5	P1
HOMER1	ENST00000282260.10	c.6-3937A>G		intron_variant		1
HOMER1	ENST00000508576.5	c.6-3937A>G		intron_variant		1
HOMER1	ENST00000535690.1	c.5+51815A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32716 AN: 151802 Hom.: 3653 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.216 AC: 32749 AN: 151922 Hom.: 3661 Cov.: 32 AF XY: 0.218 AC XY: 16194 AN XY: 74236

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.240

Alfa AF: 0.229 Hom.: 4831

Bravo AF: 0.212

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.020
DANN	Benign	0.57

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: rs10078095; hg19: chr5-78756778; COSMIC: COSV56524872;