rs10789970

chr11-113903224-C-T

Variant summary

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

The XM_024448767.2(HTR3B):c.-243+4141C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,684 control chromosomes in the GnomAD database, including 20,274 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 0.51 (20274 hom., cov: 30)
• Consequence: HTR3B XM_024448767.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

HTR3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR3B	XM_024448767.2	c.-243+4141C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.508 AC: 76956 AN: 151566 Hom.: 20230 Cov.: 30

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.508 AC: 77058 AN: 151684 Hom.: 20274 Cov.: 30 AF XY: 0.511 AC XY: 37907 AN XY: 74120

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.510

Alfa AF: 0.440 Hom.: 25729

Bravo AF: 0.521

Asia WGS AF: 0.620 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.65
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10789970; hg19: chr11-113773946;