rs2068190

Variant names:

• chr5-148627450-G-A
• rs2068190
• NM_000870.7:c.26+9539C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-148627450-G-A
• chr5-148627450-G-C
• chr5-148627450-G-T

Variant summary

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

The NM_000870.7(HTR4):​c.26+9539C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,034 control chromosomes in the GnomAD database, including 18,233 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 0.48 (18233 hom., cov: 33)
• Consequence: HTR4 NM_000870.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 9 publications found

Genes affected

HTR4 (HGNC:5299): (5-hydroxytryptamine receptor 4) This gene is a member of the family of serotonin receptors, which are G protein coupled receptors that stimulate cAMP production in response to serotonin (5-hydroxytryptamine). The gene product is a glycosylated transmembrane protein that functions in both the peripheral and central nervous system to modulate the release of various neurotransmitters. Multiple transcript variants encoding proteins with distinct C-terminal sequences have been described. [provided by RefSeq, May 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR4	NM_000870.7	c.26+9539C>T		intron_variant	Intron 2 of 6	ENST00000377888.8	NP_000861.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR4	ENST00000377888.8	c.26+9539C>T		intron_variant	Intron 2 of 6	1	NM_000870.7	ENSP00000367120.4

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73374 AN: 151916 Hom.: 18211 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.483 AC: 73444 AN: 152034 Hom.: 18233 Cov.: 33 AF XY: 0.482 AC XY: 35836 AN XY: 74324

African (AFR) AF: 0.574 AC: 23794 AN: 41448

American (AMR) AF: 0.423 AC: 6471 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3499 AN: 5166

South Asian (SAS) AF: 0.553 AC: 2661 AN: 4816

European-Finnish (FIN) AF: 0.405 AC: 4275 AN: 10552

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29600 AN: 67990

Other (OTH) AF: 0.481 AC: 1013 AN: 2104

Alfa AF: 0.451 Hom.: 66803

Bravo AF: 0.487

Asia WGS AF: 0.632 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.63
PhyloP100		0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2068190; hg19: chr5-148007013;