chr18-51721129-A-G

Position:

• chr18-51721129-A-G

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 0.0852 in 152,250 control chromosomes in the GnomAD database, including 1,389 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 0.085 (1389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0852 AC: 12955 AN: 152132 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.00598

Gnomad SAS AF: 0.00476

Gnomad FIN AF: 0.00668

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0852 AC: 12975 AN: 152250 Hom.: 1389 Cov.: 32 AF XY: 0.0825 AC XY: 6143 AN XY: 74448

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.0570

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.00599

Gnomad4 SAS AF: 0.00477

Gnomad4 FIN AF: 0.00668

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.0828

Alfa AF: 0.0469 Hom.: 126

Bravo AF: 0.0969

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7236038; hg19: chr18-49247499;