18-39944233-G-A

Variant names:

• chr18-39944233-G-A
• rs2007278

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 0.0203 in 152,192 control chromosomes in the GnomAD database, including 110 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 0.020 (110 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.113 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: 0.0202 AC: 3069 AN: 152074 Hom.: 106 Cov.: 32

Gnomad AFR AF: 0.00427

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0722

Gnomad ASJ AF: 0.00779

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0845

Gnomad FIN AF: 0.0157

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00769

Gnomad OTH AF: 0.0182

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

GnomAD4 genome AF: 0.0203 AC: 3087 AN: 152192 Hom.: 110 Cov.: 32 AF XY: 0.0236 AC XY: 1759 AN XY: 74412

African (AFR) AF: 0.00426 AC: 177 AN: 41544

American (AMR) AF: 0.0729 AC: 1114 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00779 AC: 27 AN: 3468

East Asian (EAS) AF: 0.121 AC: 622 AN: 5158

South Asian (SAS) AF: 0.0848 AC: 409 AN: 4824

European-Finnish (FIN) AF: 0.0157 AC: 166 AN: 10604

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00769 AC: 523 AN: 68000

Other (OTH) AF: 0.0204 AC: 43 AN: 2110

Alfa AF: 0.0147 Hom.: 144

Bravo AF: 0.0223

Asia WGS AF: 0.0980 AC: 340 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	2.7
DANN	Benign	0.78
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2007278; hg19: chr18-37524197;