rs1333914

Variant names:

• chr9-119820956-G-T
• rs1333914

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 0.32 in 152,034 control chromosomes in the GnomAD database, including 8,510 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 0.32 (8510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 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: 0.320 AC: 48678 AN: 151916 Hom.: 8518 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.320 AC: 48692 AN: 152034 Hom.: 8510 Cov.: 32 AF XY: 0.319 AC XY: 23741 AN XY: 74312

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.363

Alfa AF: 0.388 Hom.: 23566

Bravo AF: 0.312

Asia WGS AF: 0.329 AC: 1143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1333914; hg19: chr9-122583234; COSMIC: COSV60399929;