9-137136549-C-T

Variant names:

• chr9-137136549-C-T
• rs4880213

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 0.447 in 152,026 control chromosomes in the GnomAD database, including 15,562 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 0.45 (15562 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

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 (EAS) allele frequency at 95% confidence interval = 0.634 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: 0.447 AC: 67943 AN: 151908 Hom.: 15544 Cov.: 33

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.447 AC: 68004 AN: 152026 Hom.: 15562 Cov.: 33 AF XY: 0.454 AC XY: 33772 AN XY: 74310

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.452

Alfa AF: 0.334 Hom.: 1416

Bravo AF: 0.452

Asia WGS AF: 0.487 AC: 1691 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	0.029
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4880213; hg19: chr9-140031001;