rs9463175

Positions:

• chr6-9509797-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.422 in 151,888 control chromosomes in the GnomAD database, including 15,296 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 0.42 (15296 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.66

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.9509797C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64038 AN: 151774 Hom.: 15266 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.422 AC: 64131 AN: 151888 Hom.: 15296 Cov.: 32 AF XY: 0.416 AC XY: 30874 AN XY: 74222

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.381

Alfa AF: 0.352 Hom.: 5623

Bravo AF: 0.425

Asia WGS AF: 0.251 AC: 874 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	19
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9463175; hg19: chr6-9510030;