7-155081685-A-G

Variant names:

• chr7-155081685-A-G
• rs732050
• NM_024012.4:c.742-2470A>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.742-2470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,166 control chromosomes in the GnomAD database, including 4,949 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 0.23 (4949 hom., cov: 32)
• Consequence: HTR5A NM_024012.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.508
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HTR5A	NM_024012.4	c.742-2470A>G		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.742-2470A>G		intron_variant	Intron 1 of 1	1	NM_024012.4	ENSP00000287907.2
HTR5A	ENST00000486819.1	n.98-2470A>G		intron_variant	Intron 1 of 1	1
HTR5A	ENST00000649716.1	n.*211-2470A>G		intron_variant	Intron 2 of 2			ENSP00000497222.1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34731 AN: 152048 Hom.: 4940 Cov.: 32

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.228 AC: 34745 AN: 152166 Hom.: 4949 Cov.: 32 AF XY: 0.232 AC XY: 17224 AN XY: 74382

African (AFR) AF: 0.0561 AC: 2330 AN: 41556

American (AMR) AF: 0.222 AC: 3390 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1121 AN: 5182

South Asian (SAS) AF: 0.306 AC: 1473 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3942 AN: 10568

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20660 AN: 67988

Other (OTH) AF: 0.250 AC: 528 AN: 2114

Alfa AF: 0.281 Hom.: 3719

Bravo AF: 0.208

Asia WGS AF: 0.303 AC: 1053 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	2.1
DANN	Benign	0.73
PhyloP100		0.51
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: rs732050; hg19: chr7-154873395;