18-8931654-T-C

Variant names:

• chr18-8931654-T-C
• rs7244245

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 0.191 in 152,238 control chromosomes in the GnomAD database, including 3,627 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 0.19 (3627 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28990 AN: 152120 Hom.: 3607 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.191 AC: 29060 AN: 152238 Hom.: 3627 Cov.: 33 AF XY: 0.189 AC XY: 14091 AN XY: 74434

African (AFR) AF: 0.353 AC: 14649 AN: 41514

American (AMR) AF: 0.133 AC: 2039 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 414 AN: 3468

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5188

South Asian (SAS) AF: 0.179 AC: 862 AN: 4818

European-Finnish (FIN) AF: 0.130 AC: 1378 AN: 10618

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9077 AN: 68008

Other (OTH) AF: 0.175 AC: 371 AN: 2114

Alfa AF: 0.136 Hom.: 2534

Bravo AF: 0.196

Asia WGS AF: 0.134 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.47
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs7244245; hg19: chr18-8931652;