chr9-27630564-T-C

Position:

• chr9-27630564-T-C

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 0.287 in 152,164 control chromosomes in the GnomAD database, including 7,660 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 0.29 (7660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 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: 0.287 AC: 43639 AN: 152044 Hom.: 7654 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.287 AC: 43662 AN: 152164 Hom.: 7660 Cov.: 32 AF XY: 0.289 AC XY: 21489 AN XY: 74392

Gnomad4 AFR AF: 0.0881

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.319

Alfa AF: 0.364 Hom.: 15912

Bravo AF: 0.278

Asia WGS AF: 0.226 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12555345; hg19: chr9-27630562;