18-51155585-A-G

Position:

• chr18-51155585-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 0.477 in 152,008 control chromosomes in the GnomAD database, including 17,610 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 0.48 (17610 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.51155585A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72522 AN: 151888 Hom.: 17606 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.477 AC: 72574 AN: 152008 Hom.: 17610 Cov.: 33 AF XY: 0.473 AC XY: 35129 AN XY: 74308

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.482

Alfa AF: 0.383 Hom.: 1064

Bravo AF: 0.468

Asia WGS AF: 0.423 AC: 1469 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	17
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17736674; hg19: chr18-48681955;