rs1503428

Positions:

• chr3-87890500-G-A
• chr3-87890500-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR1F	NM_001322209.2	c.-43+68376G>A		intron_variant		ENST00000319595.7	NP_001309138.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR1F	ENST00000319595.7	c.-43+68376G>A		intron_variant			NM_001322209.2	ENSP00000322924	P1

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

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.350

Alfa AF: 0.182 Hom.: 704

Bravo AF: 0.394

Asia WGS AF: 0.276 AC: 957 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1503428; hg19: chr3-87939650;