rs9367630

Positions:

• chr6-55283305-G-A
• chr6-55283305-G-T

Variant summary

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

The XM_017010798.2(HCRTR2):​c.1331+855G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0367 in 152,238 control chromosomes in the GnomAD database, including 663 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 0.037 (663 hom., cov: 32)
• Consequence: HCRTR2 XM_017010798.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766

Genes affected

HCRTR2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCRTR2	XM_017010798.2	c.1331+855G>A		intron_variant			XP_016866287.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0366 AC: 5565 AN: 152120 Hom.: 655 Cov.: 32

Gnomad AFR AF: 0.00825

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.00547

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.0279

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00370

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0367 AC: 5585 AN: 152238 Hom.: 663 Cov.: 32 AF XY: 0.0412 AC XY: 3064 AN XY: 74412

Gnomad4 AFR AF: 0.00825

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.00547

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.0275

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.00370

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0196 Hom.: 492

Bravo AF: 0.0514

Asia WGS AF: 0.153 AC: 532 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9367630; hg19: chr6-55148103;