11-113904173-G-A

Position:

• chr11-113904173-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_024448767.2(HTR3B):​c.-243+5090G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,818 control chromosomes in the GnomAD database, including 2,178 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 0.17 (2178 hom., cov: 32)
• Consequence: HTR3B XM_024448767.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813

Genes affected

HTR3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR3B	XM_024448767.2	c.-243+5090G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25115 AN: 151702 Hom.: 2176 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.165 AC: 25122 AN: 151818 Hom.: 2178 Cov.: 32 AF XY: 0.165 AC XY: 12276 AN XY: 74198

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.181

Alfa AF: 0.174 Hom.: 701

Bravo AF: 0.160

Asia WGS AF: 0.115 AC: 400 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11214763; hg19: chr11-113774895;