NM_024012.4:c.742-5522C>A

Variant names:

• chr7-155078633-C-A
• rs4581000
• NM_024012.4:c.742-5522C>A

Variant summary

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

The NM_024012.4(HTR5A):​c.742-5522C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,136 control chromosomes in the GnomAD database, including 60,183 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 (60183 hom., cov: 32)
• Consequence: HTR5A NM_024012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 0 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=-0.83).
• 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.742-5522C>A		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	ENST00000287907.3	c.742-5522C>A		intron_variant	Intron 1 of 1	1	NM_024012.4	ENSP00000287907.2
HTR5A	ENST00000486819.1	n.97+1399C>A		intron_variant	Intron 1 of 1	1
HTR5A	ENST00000649716.1	n.*211-5522C>A		intron_variant	Intron 2 of 2			ENSP00000497222.1

Frequencies

GnomAD3 genomes AF: 0.868 AC: 131900 AN: 152018 Hom.: 60156 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.966

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.867 AC: 131974 AN: 152136 Hom.: 60183 Cov.: 32 AF XY: 0.873 AC XY: 64918 AN XY: 74402

African (AFR) AF: 0.551 AC: 22822 AN: 41456

American (AMR) AF: 0.943 AC: 14420 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3457 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5177 AN: 5178

South Asian (SAS) AF: 0.966 AC: 4668 AN: 4832

European-Finnish (FIN) AF: 1.00 AC: 10558 AN: 10560

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

European-Non Finnish (NFE) AF: 0.997 AC: 67801 AN: 68022

Other (OTH) AF: 0.892 AC: 1886 AN: 2114

Alfa AF: 0.907 Hom.: 8125

Bravo AF: 0.849

Asia WGS AF: 0.953 AC: 3306 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.9
DANN	Benign	0.81
PhyloP100		-0.18
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: rs4581000; hg19: chr7-154870343;