rs12374818

Positions:

• chr7-33654496-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 0.0455 in 152,154 control chromosomes in the GnomAD database, including 193 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 0.045 (193 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33654496G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BBS9	ENST00000672453.1	n.2476+48764G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6914 AN: 152036 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.0521

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0455 AC: 6923 AN: 152154 Hom.: 193 Cov.: 32 AF XY: 0.0443 AC XY: 3297 AN XY: 74386

Gnomad4 AFR AF: 0.0351

Gnomad4 AMR AF: 0.0521

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0333

Gnomad4 FIN AF: 0.0229

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0473 Hom.: 20

Bravo AF: 0.0472

Asia WGS AF: 0.0160 AC: 55 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.70
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12374818; hg19: chr7-33694108;