chr18-53683207-A-G

Position:

• chr18-53683207-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 0.366 in 150,428 control chromosomes in the GnomAD database, including 11,819 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 0.37 (11819 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53683207A>G		intergenic_region
LOC124904304	XR_007066375.1	n.66+60178T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.366 AC: 54948 AN: 150310 Hom.: 11791 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.366 AC: 55014 AN: 150428 Hom.: 11819 Cov.: 31 AF XY: 0.371 AC XY: 27225 AN XY: 73474

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.372

Alfa AF: 0.350 Hom.: 1937

Asia WGS AF: 0.463 AC: 1610 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.5
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9946886; hg19: chr18-51209577;