chr18-13916388-A-G

Variant names:

• chr18-13916388-A-G
• rs1893219

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 0.514 in 151,992 control chromosomes in the GnomAD database, including 21,214 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 0.51 (21214 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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: 0.514 AC: 78084 AN: 151874 Hom.: 21177 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.514 AC: 78161 AN: 151992 Hom.: 21214 Cov.: 32 AF XY: 0.512 AC XY: 37996 AN XY: 74280

African (AFR) AF: 0.682 AC: 28276 AN: 41460

American (AMR) AF: 0.425 AC: 6497 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1190 AN: 5160

South Asian (SAS) AF: 0.296 AC: 1425 AN: 4808

European-Finnish (FIN) AF: 0.519 AC: 5471 AN: 10542

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31964 AN: 67962

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.525 Hom.: 3664

Bravo AF: 0.516

Asia WGS AF: 0.300 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.53
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1893219; hg19: chr18-13916387;