rs9463175

Variant names:

• chr6-9509797-C-T
• rs9463175

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.66
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.655 AC: 27128 AN: 41408

American (AMR) AF: 0.292 AC: 4454 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3470

East Asian (EAS) AF: 0.152 AC: 785 AN: 5174

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4820

European-Finnish (FIN) AF: 0.338 AC: 3562 AN: 10538

Middle Eastern (MID) AF: 0.408 AC: 119 AN: 292

European-Non Finnish (NFE) AF: 0.354 AC: 24040 AN: 67914

Other (OTH) AF: 0.381 AC: 805 AN: 2114

Alfa AF: 0.361 Hom.: 7997

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
PhyloP100		4.7

Splicing

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

Other links and lift over

dbSNP: rs9463175; hg19: chr6-9510030;