chr5-148467144-A-G

Position:

• chr5-148467144-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000521530.6(HTR4):​c.1077-15872T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 152,018 control chromosomes in the GnomAD database, including 9,901 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 0.35 (9901 hom., cov: 32)
• Consequence: HTR4 ENST00000521530.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294

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]

LOC107986462 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986462	XR_001742935.2	n.344-1776A>G		intron_variant, non_coding_transcript_variant
HTR4	NM_001040169.2	c.1077-15872T>C		intron_variant			NP_001035259.1
HTR4	NM_199453.3	c.1077-1219T>C		intron_variant			NP_955525.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR4	ENST00000521530.6	c.1077-15872T>C		intron_variant		1		ENSP00000428320	P1
HTR4	ENST00000521735.5	c.1077-1219T>C		intron_variant		1		ENSP00000430979
HTR4	ENST00000522588.5	c.1077-1219T>C		intron_variant, NMD_transcript_variant		1		ENSP00000430874

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52580 AN: 151900 Hom.: 9902 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.346 AC: 52588 AN: 152018 Hom.: 9901 Cov.: 32 AF XY: 0.347 AC XY: 25820 AN XY: 74310

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.334

Alfa AF: 0.355 Hom.: 3735

Bravo AF: 0.351

Asia WGS AF: 0.447 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6889822; hg19: chr5-147846707;