9-127857358-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 0.548 in 149,190 control chromosomes in the GnomAD database, including 23,140 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 0.55 (23140 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 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: 0.548 AC: 81772 AN: 149084 Hom.: 23135 Cov.: 31

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.548 AC: 81803 AN: 149190 Hom.: 23140 Cov.: 31 AF XY: 0.549 AC XY: 39966 AN XY: 72798

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.566

Alfa AF: 0.596 Hom.: 60467

Bravo AF: 0.538

Asia WGS AF: 0.522 AC: 1749 AN: 3346

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.076
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7865146; hg19: chr9-130619637;