5-148448358-A-G

Variant names:

• chr5-148448358-A-G
• rs7721661
• ENST00000521530.6:c.*2827T>C

Variant summary

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

The ENST00000521530.6(HTR4):​c.*2827T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.87 (56028 hom., cov: 19)
• Consequence: HTR4 ENST00000521530.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR4	ENST00000521530.6	c.*2827T>C		3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000428320.1

Frequencies

GnomAD3 genomes AF: 0.875 AC: 127545 AN: 145816 Hom.: 55969 Cov.: 19

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.868

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.875 AC: 127652 AN: 145916 Hom.: 56028 Cov.: 19 AF XY: 0.874 AC XY: 61806 AN XY: 70744

African (AFR) AF: 0.965 AC: 37640 AN: 39006

American (AMR) AF: 0.799 AC: 11437 AN: 14314

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2903 AN: 3432

East Asian (EAS) AF: 0.775 AC: 3737 AN: 4820

South Asian (SAS) AF: 0.820 AC: 3618 AN: 4410

European-Finnish (FIN) AF: 0.887 AC: 8705 AN: 9816

Middle Eastern (MID) AF: 0.868 AC: 250 AN: 288

European-Non Finnish (NFE) AF: 0.852 AC: 57035 AN: 66966

Other (OTH) AF: 0.868 AC: 1722 AN: 1984

Alfa AF: 0.859 Hom.: 87777

Bravo AF: 0.866

Asia WGS AF: 0.830 AC: 2886 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.87
DANN	Benign	0.24
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs7721661; hg19: chr5-147827921;