rs3758987

Positions:

• chr11-113904553-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XM_024448767.2(HTR3B):​c.-242-4742T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 170,498 control chromosomes in the GnomAD database, including 8,346 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 0.32 (7694 hom., cov: 32)
  • Exomes 𝑓: 0.26 (652 hom.)
• Consequence: HTR3B XM_024448767.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

Genes affected

HTR3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR3B	XM_024448767.2	c.-242-4742T>C		intron_variant			XP_024304535.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47986 AN: 151892 Hom.: 7681 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.302

GnomAD4 exome AF: 0.257 AC: 4760 AN: 18488 Hom.: 652 AF XY: 0.257 AC XY: 2414 AN XY: 9384

Gnomad4 AFR exome AF: 0.341

Gnomad4 AMR exome AF: 0.286

Gnomad4 ASJ exome AF: 0.242

Gnomad4 EAS exome AF: 0.219

Gnomad4 SAS exome AF: 0.290

Gnomad4 FIN exome AF: 0.277

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.274

GnomAD4 genome AF: 0.316 AC: 48031 AN: 152010 Hom.: 7694 Cov.: 32 AF XY: 0.317 AC XY: 23577 AN XY: 74296

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.302

Alfa AF: 0.294 Hom.: 6276

Bravo AF: 0.315

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	20
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3758987; hg19: chr11-113775275;