3-87890500-G-A

Variant names:

• chr3-87890500-G-A
• rs1503428
• NM_001322209.2:c.-43+68376G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001322209.2(HTR1F):​c.-43+68376G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 149,636 control chromosomes in the GnomAD database, including 15,251 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 0.38 (15251 hom., cov: 31)
• Consequence: HTR1F NM_001322209.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 0 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322209.2. 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
	HTR1F	NM_001322209.2	MANE Select	c.-43+68376G>A		intron	N/A	NP_001309138.1
	HTR1F	NM_001322208.2		c.-43+68376G>A		intron	N/A	NP_001309137.1
	HTR1F	NM_001322210.2		c.-43+68376G>A		intron	N/A	NP_001309139.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR1F	ENST00000319595.7	TSL:6 MANE Select	c.-43+68376G>A		intron	N/A	ENSP00000322924.4

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56067 AN: 149546 Hom.: 15198 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.270

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.375 AC: 56169 AN: 149636 Hom.: 15251 Cov.: 31 AF XY: 0.375 AC XY: 27268 AN XY: 72796

African (AFR) AF: 0.772 AC: 31812 AN: 41226

American (AMR) AF: 0.279 AC: 4177 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 782 AN: 3460

East Asian (EAS) AF: 0.390 AC: 1981 AN: 5082

South Asian (SAS) AF: 0.170 AC: 794 AN: 4678

European-Finnish (FIN) AF: 0.231 AC: 2204 AN: 9532

Middle Eastern (MID) AF: 0.270 AC: 75 AN: 278

European-Non Finnish (NFE) AF: 0.199 AC: 13418 AN: 67402

Other (OTH) AF: 0.350 AC: 729 AN: 2080

Alfa AF: 0.193 Hom.: 1430

Bravo AF: 0.394

Asia WGS AF: 0.276 AC: 957 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.16
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1503428; hg19: chr3-87939650;