9-137002712-C-T

Position:

• chr9-137002712-C-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 0.71 in 152,202 control chromosomes in the GnomAD database, including 38,581 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 0.71 (38581 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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 = 0.79 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: 0.710 AC: 107985 AN: 152084 Hom.: 38552 Cov.: 34

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.710 AC: 108068 AN: 152202 Hom.: 38581 Cov.: 34 AF XY: 0.709 AC XY: 52760 AN XY: 74432

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.713

Alfa AF: 0.692 Hom.: 6433

Bravo AF: 0.711

Asia WGS AF: 0.770 AC: 2677 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	0.16
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: rs2049040; hg19: chr9-139897164;