chr18-59212595-T-C

Variant names:

• chr18-59212595-T-C
• rs9319943

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 0.249 in 151,962 control chromosomes in the GnomAD database, including 5,119 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 0.25 (5119 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 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: 0.249 AC: 37768 AN: 151844 Hom.: 5106 Cov.: 30

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.249 AC: 37821 AN: 151962 Hom.: 5119 Cov.: 30 AF XY: 0.252 AC XY: 18725 AN XY: 74270

African (AFR) AF: 0.349 AC: 14443 AN: 41440

American (AMR) AF: 0.251 AC: 3833 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 789 AN: 3470

East Asian (EAS) AF: 0.189 AC: 973 AN: 5154

South Asian (SAS) AF: 0.244 AC: 1175 AN: 4806

European-Finnish (FIN) AF: 0.277 AC: 2921 AN: 10546

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12887 AN: 67950

Other (OTH) AF: 0.239 AC: 506 AN: 2114

Alfa AF: 0.212 Hom.: 7138

Bravo AF: 0.255

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs9319943; hg19: chr18-56879827;