18-12300937-T-C

Variant names:

• chr18-12300937-T-C
• rs9807444

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 0.144 in 152,278 control chromosomes in the GnomAD database, including 1,675 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 0.14 (1675 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 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: 0.144 AC: 21928 AN: 152160 Hom.: 1675 Cov.: 33

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.144 AC: 21942 AN: 152278 Hom.: 1675 Cov.: 33 AF XY: 0.144 AC XY: 10725 AN XY: 74446

African (AFR) AF: 0.197 AC: 8180 AN: 41542

American (AMR) AF: 0.169 AC: 2592 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 560 AN: 3468

East Asian (EAS) AF: 0.157 AC: 814 AN: 5186

South Asian (SAS) AF: 0.131 AC: 630 AN: 4822

European-Finnish (FIN) AF: 0.0861 AC: 914 AN: 10610

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7737 AN: 68034

Other (OTH) AF: 0.162 AC: 342 AN: 2116

Alfa AF: 0.126 Hom.: 4997

Bravo AF: 0.152

Asia WGS AF: 0.147 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.83
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs9807444; hg19: chr18-12300936;