chr18-57399314-A-G

Variant names:

• chr18-57399314-A-G
• rs221877

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.233 in 152,056 control chromosomes in the GnomAD database, including 6,043 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 0.23 (6043 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 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: 0.233 AC: 35350 AN: 151938 Hom.: 6025 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.233 AC: 35417 AN: 152056 Hom.: 6043 Cov.: 32 AF XY: 0.230 AC XY: 17117 AN XY: 74366

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.180

Alfa AF: 0.135 Hom.: 3477

Bravo AF: 0.245

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs221877; hg19: chr18-55066546;