rs894520

Variant names:

• chr9-38189530-T-C
• rs894520

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 0.365 in 151,988 control chromosomes in the GnomAD database, including 10,417 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 0.36 (10417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 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: 0.364 AC: 55355 AN: 151870 Hom.: 10404 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.365 AC: 55405 AN: 151988 Hom.: 10417 Cov.: 32 AF XY: 0.361 AC XY: 26783 AN XY: 74280

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.351

Alfa AF: 0.328 Hom.: 11910

Bravo AF: 0.370

Asia WGS AF: 0.359 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs894520; hg19: chr9-38189527;