ENST00000486819.1:n.32G>C

Variant names:

• chr7-155077169-G-C
• rs1440451
• ENST00000486819.1:n.32G>C

Variant summary

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

The ENST00000486819.1(HTR5A):​n.32G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,212 control chromosomes in the GnomAD database, including 60,384 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 0.87 (60384 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: HTR5A ENST00000486819.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692
• Publications: 1 publications found

Genes affected

HTR5A (HGNC:5300): (5-hydroxytryptamine receptor 5A) The neurotransmitter serotonin (5-hydroxytryptamine, 5-HT) has been implicated in a wide range of psychiatric conditions and also has vasoconstrictive and vasodilatory effects. The gene described in this record is a member of 5-hydroxytryptamine (serotonin) receptor family and encodes a multi-pass membrane protein that functions as a receptor for 5-hydroxytryptamine and couples to G-proteins. This protein has been shown to function in part through the regulation of intracellular Ca2+ mobilization. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR5A	NM_024012.4	c.741+5529G>C		intron_variant	Intron 1 of 1	ENST00000287907.3	NP_076917.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HTR5A	ENST00000486819.1	n.32G>C		non_coding_transcript_exon_variant	Exon 1 of 2	1
HTR5A	ENST00000287907.3	c.741+5529G>C		intron_variant	Intron 1 of 1	1	NM_024012.4	ENSP00000287907.2
HTR5A	ENST00000649716.1	n.*210+4728G>C		intron_variant	Intron 2 of 2			ENSP00000497222.1

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132153 AN: 152094 Hom.: 60357 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.892

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.869 AC: 132226 AN: 152212 Hom.: 60384 Cov.: 32 AF XY: 0.874 AC XY: 65061 AN XY: 74406

African (AFR) AF: 0.551 AC: 22850 AN: 41458

American (AMR) AF: 0.943 AC: 14425 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3455 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5187 AN: 5188

South Asian (SAS) AF: 0.995 AC: 4807 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10616 AN: 10618

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.997 AC: 67811 AN: 68030

Other (OTH) AF: 0.893 AC: 1890 AN: 2116

Alfa AF: 0.902 Hom.: 3537

Bravo AF: 0.849

Asia WGS AF: 0.974 AC: 3386 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	0.57
DANN	Benign	0.44
PhyloP100		-0.69
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: rs1440451; hg19: chr7-154868879;