7-155070881-G-C

Position:

• chr7-155070881-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR5A	NM_024012.4	c.-19G>C		5_prime_UTR_variant	1/2	ENST00000287907.3	NP_076917.1
HTR5A-AS1	NR_038945.1	n.524+153C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR5A	ENST00000287907.3	c.-19G>C		5_prime_UTR_variant	1/2	1	NM_024012.4	ENSP00000287907	P1
HTR5A-AS1	ENST00000671665.1	n.1417+153C>G		intron_variant, non_coding_transcript_variant

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

GnomAD3 exomes AF: 0.418 AC: 97363 AN: 232648 Hom.: 21136 AF XY: 0.415 AC XY: 52355 AN XY: 126024

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 SAS exome AF: 0.450

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

Gnomad4 AFR exome AF: 0.399

Gnomad4 AMR exome AF: 0.503

Gnomad4 ASJ exome AF: 0.404

Gnomad4 EAS exome AF: 0.481

Gnomad4 SAS exome AF: 0.446

Gnomad4 FIN exome AF: 0.467

Gnomad4 NFE exome AF: 0.347

Gnomad4 OTH exome AF: 0.388

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

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.379

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
DANN	Benign	0.82

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800883; hg19: chr7-154862591; COSMIC: COSV55281128; COSMIC: COSV55281128;