11-113899633-G-A

Position:

• chr11-113899633-G-A

Variant summary

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

The XM_024448767.2(HTR3B):​c.-243+550G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,144 control chromosomes in the GnomAD database, including 39,827 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 0.71 (39827 hom., cov: 33)
• Consequence: HTR3B XM_024448767.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44

Genes affected

HTR3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR3B	XM_024448767.2	c.-243+550G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107967 AN: 152026 Hom.: 39764 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.710 AC: 108089 AN: 152144 Hom.: 39827 Cov.: 33 AF XY: 0.713 AC XY: 53006 AN XY: 74348

Gnomad4 AFR AF: 0.913

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.722

Alfa AF: 0.620 Hom.: 32715

Bravo AF: 0.724

Asia WGS AF: 0.745 AC: 2591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	21
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1176758; hg19: chr11-113770355;