9-30654172-C-G

Variant names:

• chr9-30654172-C-G
• rs12552047

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 0.0713 in 151,704 control chromosomes in the GnomAD database, including 540 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 0.071 (540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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: 0.0714 AC: 10823 AN: 151588 Hom.: 540 Cov.: 32

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0713 AC: 10819 AN: 151704 Hom.: 540 Cov.: 32 AF XY: 0.0700 AC XY: 5192 AN XY: 74172

African (AFR) AF: 0.0193 AC: 800 AN: 41478

American (AMR) AF: 0.0694 AC: 1053 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3460

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4818

European-Finnish (FIN) AF: 0.0767 AC: 814 AN: 10612

Middle Eastern (MID) AF: 0.0862 AC: 25 AN: 290

European-Non Finnish (NFE) AF: 0.107 AC: 7259 AN: 67674

Other (OTH) AF: 0.0808 AC: 170 AN: 2104

Alfa AF: 0.0781 Hom.: 76

Bravo AF: 0.0700

Asia WGS AF: 0.0140 AC: 50 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs12552047; hg19: chr9-30654170; COSMIC: COSV60350313;