chr5-148464829-G-T

Position:

• chr5-148464829-G-T

Variant summary

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

The XR_001742935.2(LOC107986462):​n.344-4091G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,956 control chromosomes in the GnomAD database, including 11,857 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 (11857 hom., cov: 32)
• Consequence: LOC107986462 XR_001742935.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986462	XR_001742935.2	n.344-4091G>T		intron_variant, non_coding_transcript_variant
HTR4	NM_001040169.2	c.1077-13557C>A		intron_variant			NP_001035259.1
HTR4	NM_199453.3	c.*15+1021C>A		intron_variant			NP_955525.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR4	ENST00000521530.6	c.1077-13557C>A		intron_variant		1		ENSP00000428320	P1
HTR4	ENST00000521735.5	c.*15+1021C>A		intron_variant		1		ENSP00000430979
HTR4	ENST00000522588.5	c.*15+1021C>A		intron_variant, NMD_transcript_variant		1		ENSP00000430874

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57302 AN: 151838 Hom.: 11851 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.377 AC: 57325 AN: 151956 Hom.: 11857 Cov.: 32 AF XY: 0.381 AC XY: 28291 AN XY: 74256

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.373

Alfa AF: 0.409 Hom.: 5416

Bravo AF: 0.386

Asia WGS AF: 0.542 AC: 1879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7735184; hg19: chr5-147844392;