5-79496521-C-T

Position:

• chr5-79496521-C-T

Variant summary

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

The NM_004272.5(HOMER1):​c.5+16249G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,014 control chromosomes in the GnomAD database, including 4,409 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 0.23 (4409 hom., cov: 31)
• Consequence: HOMER1 NM_004272.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HOMER1	NM_004272.5	c.5+16249G>A		intron_variant		ENST00000334082.11	NP_004263.1
HOMER1	NM_001277077.1	c.5+16249G>A		intron_variant			NP_001264006.1
HOMER1	NM_001277078.1	c.5+16249G>A		intron_variant			NP_001264007.1
HOMER1	XM_017010059.3	c.5+16249G>A		intron_variant			XP_016865548.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HOMER1	ENST00000334082.11	c.5+16249G>A		intron_variant		1	NM_004272.5	ENSP00000334382	P1
HOMER1	ENST00000282260.10	c.5+16249G>A		intron_variant		1		ENSP00000282260
HOMER1	ENST00000508576.5	c.5+16249G>A		intron_variant		1		ENSP00000426651
HOMER1	ENST00000535690.1	c.5+16249G>A		intron_variant		1		ENSP00000441587

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34743 AN: 151898 Hom.: 4408 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.229 AC: 34769 AN: 152014 Hom.: 4409 Cov.: 31 AF XY: 0.234 AC XY: 17395 AN XY: 74298

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.256

Alfa AF: 0.241 Hom.: 901

Bravo AF: 0.219

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs6871510; hg19: chr5-78792344; COSMIC: COSV56530406;