chr9-27232750-C-T

Variant names:

• chr9-27232750-C-T
• rs1322048

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 0.381 in 151,946 control chromosomes in the GnomAD database, including 11,884 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 0.38 (11884 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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: 0.381 AC: 57779 AN: 151828 Hom.: 11862 Cov.: 31

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.381 AC: 57862 AN: 151946 Hom.: 11884 Cov.: 31 AF XY: 0.374 AC XY: 27800 AN XY: 74292

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.396

Alfa AF: 0.337 Hom.: 17845

Bravo AF: 0.397

Asia WGS AF: 0.222 AC: 772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1322048; hg19: chr9-27232748;