9-27232750-C-T

Variant names:

• chr9-27232750-C-T
• rs1322048

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.524 AC: 21672 AN: 41388

American (AMR) AF: 0.399 AC: 6098 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1031 AN: 3464

East Asian (EAS) AF: 0.152 AC: 787 AN: 5164

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4814

European-Finnish (FIN) AF: 0.283 AC: 2992 AN: 10564

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22693 AN: 67958

Other (OTH) AF: 0.396 AC: 835 AN: 2110

Alfa AF: 0.345 Hom.: 39084

Bravo AF: 0.397

Asia WGS AF: 0.222 AC: 772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.36
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1322048; hg19: chr9-27232748;