rs9469457

Positions:

• chr6-33522105-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 0.0385 in 152,224 control chromosomes in the GnomAD database, including 265 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 0.038 (265 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.33522105G>A		intergenic_region
LOC107986537	XR_001743876.1	n.18-2614C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5842 AN: 152106 Hom.: 262 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00733

Gnomad SAS AF: 0.0133

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00878

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0385 AC: 5858 AN: 152224 Hom.: 265 Cov.: 32 AF XY: 0.0382 AC XY: 2847 AN XY: 74442

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.00878

Gnomad4 OTH AF: 0.0345

Alfa AF: 0.0233 Hom.: 39

Bravo AF: 0.0442

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
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: rs9469457; hg19: chr6-33489882;