rs6475526

Variant names:

• chr9-21242162-C-T
• rs6475526

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.334 in 151,982 control chromosomes in the GnomAD database, including 8,702 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 0.33 (8702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.499 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: 0.334 AC: 50793 AN: 151862 Hom.: 8700 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.334 AC: 50810 AN: 151982 Hom.: 8702 Cov.: 32 AF XY: 0.337 AC XY: 25006 AN XY: 74300

African (AFR) AF: 0.265 AC: 11000 AN: 41440

American (AMR) AF: 0.315 AC: 4813 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1198 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1736 AN: 5174

South Asian (SAS) AF: 0.516 AC: 2489 AN: 4824

European-Finnish (FIN) AF: 0.367 AC: 3872 AN: 10546

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24483 AN: 67946

Other (OTH) AF: 0.355 AC: 749 AN: 2108

Alfa AF: 0.359 Hom.: 9032

Bravo AF: 0.325

Asia WGS AF: 0.445 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.81
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs6475526; hg19: chr9-21242161; COSMIC: COSV66516405;