3-87982686-G-T

Variant names:

• chr3-87982686-G-T
• rs6781226
• NM_001322209.2:c.-42-8022G>T

Variant summary

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

The NM_000866.5(HTR1F):​c.-48G>T variant causes a 5 prime UTR premature start codon gain 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: HTR1F NM_000866.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 2 publications found

Genes affected

HTR1F (HGNC:5292): (5-hydroxytryptamine receptor 1F) Enables G protein-coupled serotonin receptor activity and serotonin binding activity. Involved in adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000866.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR1F	NM_001322209.2	MANE Select	c.-42-8022G>T		intron	N/A	NP_001309138.1	P30939
	HTR1F	NM_000866.5		c.-48G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 2	NP_000857.1	P30939
	HTR1F	NM_000866.5		c.-48G>T		5_prime_UTR	Exon 1 of 2	NP_000857.1	P30939

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR1F	ENST00000319595.7	TSL:6 MANE Select	c.-42-8022G>T		intron	N/A	ENSP00000322924.4	P30939
	HTR1F	ENST00000858974.1		c.-42-8022G>T		intron	N/A	ENSP00000529033.1

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
DANN	Benign	0.45
PhyloP100		-0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6781226; hg19: chr3-88031836;