7-155082862-A-G

Variant names:

• chr7-155082862-A-G
• rs2698512
• NM_024012.4:c.742-1293A>G

Variant summary

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

The NM_024012.4(HTR5A):​c.742-1293A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,164 control chromosomes in the GnomAD database, including 55,780 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 0.84 (55780 hom., cov: 32)
• Consequence: HTR5A NM_024012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024012.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR5A	NM_024012.4	MANE Select	c.742-1293A>G		intron	N/A	NP_076917.1	A4D2N2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR5A	ENST00000287907.3	TSL:1 MANE Select	c.742-1293A>G		intron	N/A	ENSP00000287907.2	P47898
	HTR5A	ENST00000486819.1	TSL:1	n.98-1293A>G		intron	N/A
	HTR5A	ENST00000649716.1		n.*211-1293A>G		intron	N/A	ENSP00000497222.1	A0A3B3ISH0

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127720 AN: 152046 Hom.: 55763 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.840 AC: 127780 AN: 152164 Hom.: 55780 Cov.: 32 AF XY: 0.843 AC XY: 62759 AN XY: 74404

African (AFR) AF: 0.580 AC: 24035 AN: 41440

American (AMR) AF: 0.857 AC: 13110 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3247 AN: 3472

East Asian (EAS) AF: 0.833 AC: 4306 AN: 5172

South Asian (SAS) AF: 0.940 AC: 4539 AN: 4830

European-Finnish (FIN) AF: 0.973 AC: 10330 AN: 10620

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65301 AN: 68020

Other (OTH) AF: 0.860 AC: 1817 AN: 2114

Alfa AF: 0.882 Hom.: 10182

Bravo AF: 0.816

Asia WGS AF: 0.882 AC: 3063 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2698512; hg19: chr7-154874572;