rs13356332

Variant names:

• chr5-79450876-C-G
• rs13356332
• NM_004272.5:c.294+114G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-79450876-C-G
• chr5-79450876-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004272.5(HOMER1):​c.294+114G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000383 in 1,043,852 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: HOMER1 NM_004272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.780
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HOMER1	NM_004272.5	c.294+114G>C		intron_variant	Intron 3 of 8	ENST00000334082.11	NP_004263.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HOMER1	ENST00000334082.11	c.294+114G>C		intron_variant	Intron 3 of 8	1	NM_004272.5	ENSP00000334382.6
HOMER1	ENST00000282260.10	c.294+114G>C		intron_variant	Intron 3 of 5	1		ENSP00000282260.6
HOMER1	ENST00000535690.1	c.6-48821G>C		intron_variant	Intron 1 of 4	1		ENSP00000441587.1
HOMER1	ENST00000508576.5	c.294+114G>C		intron_variant	Intron 3 of 5	1		ENSP00000426651.1

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 151962 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000336 AC: 3 AN: 891890 Hom.: 0 AF XY: 0.00000450 AC XY: 2 AN XY: 444076

African (AFR) AF: 0.00 AC: 0 AN: 21072

American (AMR) AF: 0.00 AC: 0 AN: 22220

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16902

East Asian (EAS) AF: 0.00 AC: 0 AN: 32780

South Asian (SAS) AF: 0.0000640 AC: 3 AN: 46842

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32394

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4080

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 675630

Other (OTH) AF: 0.00 AC: 0 AN: 39970

GnomAD4 genome AF: 0.00000658 AC: 1 AN: 151962 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74202

African (AFR) AF: 0.00 AC: 0 AN: 41380

American (AMR) AF: 0.00 AC: 0 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10534

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67978

Other (OTH) AF: 0.00 AC: 0 AN: 2088

Alfa AF: 0.00 Hom.: 319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		0.78

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: rs13356332; hg19: chr5-78746699;