rs6871510

Positions:

• chr5-79496521-C-G
• chr5-79496521-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_004272.5(HOMER1):​c.5+16249G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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;