rs1330320

chr9-21255151-A-Gchr9-21255151-A-T

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 0.4 in 151,908 control chromosomes in the GnomAD database, including 12,295 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 0.40 (12295 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60707 AN: 151790 Hom.: 12281 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.400 AC: 60764 AN: 151908 Hom.: 12295 Cov.: 31 AF XY: 0.399 AC XY: 29637 AN XY: 74256

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.391

Alfa AF: 0.393 Hom.: 24186

Bravo AF: 0.405

Asia WGS AF: 0.403 AC: 1402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.51
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1330320; hg19: chr9-21255150; COSMIC: COSV69450713;