rs1328685

Positions:

• chr13-46897755-G-A
• chr13-46897755-G-C
• chr13-46897755-G-T

Variant summary

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

The NM_001378924.1(HTR2A):​c.-329+197C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,178 control chromosomes in the GnomAD database, including 57,332 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 0.87 (57332 hom., cov: 31)
• Consequence: HTR2A NM_001378924.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

HTR2A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR2A	NM_001378924.1	c.-329+197C>T		intron_variant			NP_001365853.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131652 AN: 152060 Hom.: 57286 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.866 AC: 131753 AN: 152178 Hom.: 57332 Cov.: 31 AF XY: 0.868 AC XY: 64581 AN XY: 74386

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.894

Gnomad4 ASJ AF: 0.852

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.859

Alfa AF: 0.890 Hom.: 59014

Bravo AF: 0.858

Asia WGS AF: 0.932 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.062
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328685; hg19: chr13-47471890;