5-79496521-C-T

Variant names:

• chr5-79496521-C-T
• rs6871510
• NM_004272.5:c.5+16249G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004272.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOMER1	NM_004272.5	MANE Select	c.5+16249G>A		intron	N/A	NP_004263.1
	HOMER1	NM_001277077.1		c.5+16249G>A		intron	N/A	NP_001264006.1
	HOMER1	NM_001277078.1		c.5+16249G>A		intron	N/A	NP_001264007.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HOMER1	ENST00000334082.11	TSL:1 MANE Select	c.5+16249G>A		intron	N/A	ENSP00000334382.6
	HOMER1	ENST00000282260.10	TSL:1	c.5+16249G>A		intron	N/A	ENSP00000282260.6
	HOMER1	ENST00000535690.1	TSL:1	c.5+16249G>A		intron	N/A	ENSP00000441587.1

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

African (AFR) AF: 0.132 AC: 5459 AN: 41494

American (AMR) AF: 0.237 AC: 3611 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1143 AN: 3470

East Asian (EAS) AF: 0.380 AC: 1962 AN: 5158

South Asian (SAS) AF: 0.419 AC: 2011 AN: 4800

European-Finnish (FIN) AF: 0.248 AC: 2613 AN: 10556

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17206 AN: 67956

Other (OTH) AF: 0.256 AC: 540 AN: 2108

Alfa AF: 0.242 Hom.: 1531

Bravo AF: 0.219

Asia WGS AF: 0.402 AC: 1395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.29
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6871510; hg19: chr5-78792344; COSMIC: COSV56530406;