7-155070881-G-C

Variant names:

• chr7-155070881-G-C
• rs1800883
• NM_024012.4:c.-19G>C

Variant summary

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

The NM_024012.4(HTR5A):​c.-19G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 1,584,366 control chromosomes in the GnomAD database, including 111,682 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 0.39 (11993 hom., cov: 32)
  • Exomes 𝑓: 0.37 (99689 hom.)
• Consequence: HTR5A NM_024012.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 19 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]

HTR5A-AS1 (HGNC:48956): (HTR5A antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 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.-19G>C		5_prime_UTR	Exon 1 of 2	NP_076917.1	A4D2N2
	HTR5A-AS1	NR_038945.1		n.524+153C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR5A	ENST00000287907.3	TSL:1 MANE Select	c.-19G>C		5_prime_UTR	Exon 1 of 2	ENSP00000287907.2	P47898
	HTR5A-AS1	ENST00000395731.5	TSL:1	n.524+153C>G		intron	N/A
	HTR5A-AS1	ENST00000493904.3	TSL:4	n.551+153C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59790 AN: 151850 Hom.: 11966 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.373

GnomAD2 exomes AF: 0.418 AC: 97363 AN: 232648 AF XY: 0.415

Gnomad AFR exome AF: 0.403

Gnomad AMR exome AF: 0.510

Gnomad ASJ exome AF: 0.405

Gnomad EAS exome AF: 0.515

Gnomad FIN exome AF: 0.464

Gnomad NFE exome AF: 0.365

Gnomad OTH exome AF: 0.401

GnomAD4 exome AF: 0.369 AC: 527892 AN: 1432398 Hom.: 99689 Cov.: 35 AF XY: 0.370 AC XY: 263059 AN XY: 710636

African (AFR) AF: 0.399 AC: 13261 AN: 33238

American (AMR) AF: 0.503 AC: 22184 AN: 44142

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 10184 AN: 25186

East Asian (EAS) AF: 0.481 AC: 18965 AN: 39452

South Asian (SAS) AF: 0.446 AC: 37449 AN: 84006

European-Finnish (FIN) AF: 0.467 AC: 18437 AN: 39486

Middle Eastern (MID) AF: 0.350 AC: 1995 AN: 5696

European-Non Finnish (NFE) AF: 0.347 AC: 382291 AN: 1101574

Other (OTH) AF: 0.388 AC: 23126 AN: 59618

GnomAD4 genome AF: 0.394 AC: 59865 AN: 151968 Hom.: 11993 Cov.: 32 AF XY: 0.400 AC XY: 29709 AN XY: 74276

African (AFR) AF: 0.405 AC: 16764 AN: 41440

American (AMR) AF: 0.419 AC: 6403 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1380 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2674 AN: 5146

South Asian (SAS) AF: 0.458 AC: 2205 AN: 4818

European-Finnish (FIN) AF: 0.475 AC: 5010 AN: 10556

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24219 AN: 67948

Other (OTH) AF: 0.379 AC: 800 AN: 2112

Alfa AF: 0.379 Hom.: 2034

Bravo AF: 0.394

Asia WGS AF: 0.512 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
DANN	Benign	0.82
PhyloP100		0.14
Mutation Taster		=298/2	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: rs1800883; hg19: chr7-154862591; COSMIC: COSV55281128; COSMIC: COSV55281128;