NM_004272.5:c.6-3937A>G

Variant names:

• chr5-79460955-T-C
• rs10078095
• NM_004272.5:c.6-3937A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HOMER1	NM_004272.5	c.6-3937A>G		intron_variant	Intron 1 of 8	ENST00000334082.11	NP_004263.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HOMER1	ENST00000334082.11	c.6-3937A>G		intron_variant	Intron 1 of 8	1	NM_004272.5	ENSP00000334382.6
HOMER1	ENST00000282260.10	c.6-3937A>G		intron_variant	Intron 1 of 5	1		ENSP00000282260.6
HOMER1	ENST00000535690.1	c.5+51815A>G		intron_variant	Intron 1 of 4	1		ENSP00000441587.1
HOMER1	ENST00000508576.5	c.6-3937A>G		intron_variant	Intron 1 of 5	1		ENSP00000426651.1

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

African (AFR) AF: 0.189 AC: 7830 AN: 41414

American (AMR) AF: 0.221 AC: 3367 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3468

East Asian (EAS) AF: 0.142 AC: 731 AN: 5160

South Asian (SAS) AF: 0.369 AC: 1775 AN: 4816

European-Finnish (FIN) AF: 0.168 AC: 1770 AN: 10538

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15619 AN: 67948

Other (OTH) AF: 0.240 AC: 506 AN: 2106

Alfa AF: 0.226 Hom.: 11442

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
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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