rs4597955

Variant names:

• chr5-148467710-G-A
• rs4597955
• ENST00000521530.6:c.1077-16438C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-148467710-G-A
• chr5-148467710-G-C
• chr5-148467710-G-T

Variant summary

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

The NM_001040169.2(HTR4):​c.1077-16438C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,184 control chromosomes in the GnomAD database, including 39,339 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 0.70 (39339 hom., cov: 33)
• Consequence: HTR4 NM_001040169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 11 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]

ENSG00000300418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040169.2. 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
	HTR4	NM_001040169.2		c.1077-16438C>T		intron	N/A	NP_001035259.1	Q13639-2
	HTR4	NM_199453.3		c.1077-1785C>T		intron	N/A	NP_955525.1	Q13639-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR4	ENST00000521530.6	TSL:1	c.1077-16438C>T		intron	N/A	ENSP00000428320.1	Q13639-2
	HTR4	ENST00000521735.5	TSL:1	c.1077-1785C>T		intron	N/A	ENSP00000430979.1	Q13639-5
	HTR4	ENST00000522588.5	TSL:1	n.1077-1785C>T		intron	N/A	ENSP00000430874.1	Q13639-5

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106720 AN: 152066 Hom.: 39271 Cov.: 33

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.702 AC: 106847 AN: 152184 Hom.: 39339 Cov.: 33 AF XY: 0.703 AC XY: 52287 AN XY: 74394

African (AFR) AF: 0.915 AC: 38042 AN: 41554

American (AMR) AF: 0.716 AC: 10948 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1982 AN: 3468

East Asian (EAS) AF: 0.931 AC: 4831 AN: 5188

South Asian (SAS) AF: 0.651 AC: 3137 AN: 4820

European-Finnish (FIN) AF: 0.586 AC: 6190 AN: 10564

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39600 AN: 67982

Other (OTH) AF: 0.656 AC: 1387 AN: 2114

Alfa AF: 0.611 Hom.: 48525

Bravo AF: 0.722

Asia WGS AF: 0.810 AC: 2813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.0
DANN	Benign	0.46
PhyloP100		0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4597955; hg19: chr5-147847273;