rs13432259

chr2-117887500-G-Achr2-117887500-G-T

Variant summary

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

The ENST00000430851.1(HTR5BP):n.819-15503G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0882 in 152,180 control chromosomes in the GnomAD database, including 667 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 0.088 (667 hom., cov: 32)
• Consequence: HTR5BP ENST00000430851.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

Genes affected

HTR5BP (HGNC:16291): (5-hydroxytryptamine receptor 5B, pseudogene)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR5BP	ENST00000430851.1	n.819-15503G>A		intron_variant, non_coding_transcript_variant
	ENST00000434708.1	n.114-15503G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0880 AC: 13380 AN: 152062 Hom.: 660 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0255

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.0729

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

GnomAD4 genome AF: 0.0882 AC: 13425 AN: 152180 Hom.: 667 Cov.: 32 AF XY: 0.0922 AC XY: 6856 AN XY: 74394

Gnomad4 AFR AF: 0.0966

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.0471

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.0739

Gnomad4 OTH AF: 0.0783

Alfa AF: 0.0676 Hom.: 207

Bravo AF: 0.0859

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.7
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13432259; hg19: chr2-118645076;