rs1465648

Variant names:

• chr3-87901079-C-T
• rs1465648
• NM_001322209.2:c.-43+78955C>T

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+78955C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,034 control chromosomes in the GnomAD database, including 15,554 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 (15554 hom., cov: 31)
• Consequence: HTR1F NM_001322209.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 8 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR1F	NM_001322209.2	c.-43+78955C>T		intron_variant	Intron 2 of 2	ENST00000319595.7	NP_001309138.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR1F	ENST00000319595.7	c.-43+78955C>T		intron_variant	Intron 2 of 2	6	NM_001322209.2	ENSP00000322924.4

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57850 AN: 151914 Hom.: 15499 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.381 AC: 57960 AN: 152034 Hom.: 15554 Cov.: 31 AF XY: 0.379 AC XY: 28171 AN XY: 74294

African (AFR) AF: 0.769 AC: 31913 AN: 41476

American (AMR) AF: 0.282 AC: 4302 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3464

East Asian (EAS) AF: 0.250 AC: 1290 AN: 5164

South Asian (SAS) AF: 0.162 AC: 782 AN: 4814

European-Finnish (FIN) AF: 0.271 AC: 2859 AN: 10564

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 14995 AN: 67976

Other (OTH) AF: 0.349 AC: 737 AN: 2110

Alfa AF: 0.264 Hom.: 17477

Bravo AF: 0.400

Asia WGS AF: 0.227 AC: 789 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.18
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1465648; hg19: chr3-87950229;