5-79467522-T-C

Variant names:

• chr5-79467522-T-C
• rs4323213
• NM_004272.5:c.6-10504A>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.6-10504A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,854 control chromosomes in the GnomAD database, including 23,519 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 0.54 (23519 hom., cov: 31)
• Consequence: HOMER1 NM_004272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HOMER1	NM_004272.5	c.6-10504A>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.6-10504A>G		intron_variant	Intron 1 of 8	1	NM_004272.5	ENSP00000334382.6
HOMER1	ENST00000282260.10	c.6-10504A>G		intron_variant	Intron 1 of 5	1		ENSP00000282260.6
HOMER1	ENST00000535690.1	c.5+45248A>G		intron_variant	Intron 1 of 4	1		ENSP00000441587.1
HOMER1	ENST00000508576.5	c.6-10504A>G		intron_variant	Intron 1 of 5	1		ENSP00000426651.1

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82524 AN: 151744 Hom.: 23497 Cov.: 31

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.544 AC: 82593 AN: 151854 Hom.: 23519 Cov.: 31 AF XY: 0.550 AC XY: 40830 AN XY: 74238

African (AFR) AF: 0.675 AC: 27958 AN: 41390

American (AMR) AF: 0.620 AC: 9473 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3466

East Asian (EAS) AF: 0.707 AC: 3657 AN: 5176

South Asian (SAS) AF: 0.714 AC: 3437 AN: 4816

European-Finnish (FIN) AF: 0.404 AC: 4243 AN: 10502

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.445 AC: 30233 AN: 67922

Other (OTH) AF: 0.568 AC: 1200 AN: 2112

Alfa AF: 0.485 Hom.: 77683

Bravo AF: 0.567

Asia WGS AF: 0.729 AC: 2531 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.80
PhyloP100		-0.97
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: rs4323213; hg19: chr5-78763345; COSMIC: COSV56529889;