rs1362927

Positions:

• chr7-33777097-G-A

Variant summary

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

The variant allele was found at a frequency of 0.79 in 152,060 control chromosomes in the GnomAD database, including 48,085 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 0.79 (48085 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33777097G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BBS9	ENST00000672453.1	n.2477-4661G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120038 AN: 151942 Hom.: 48077 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.790 AC: 120076 AN: 152060 Hom.: 48085 Cov.: 31 AF XY: 0.778 AC XY: 57793 AN XY: 74322

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.806

Alfa AF: 0.828 Hom.: 103682

Bravo AF: 0.783

Asia WGS AF: 0.575 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.59
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1362927; hg19: chr7-33816709;