chr18-53771373-G-A

Position:

• chr18-53771373-G-A

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 0.24 in 151,884 control chromosomes in the GnomAD database, including 4,803 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 0.24 (4803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36351 AN: 151766 Hom.: 4792 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.240 AC: 36413 AN: 151884 Hom.: 4803 Cov.: 32 AF XY: 0.237 AC XY: 17586 AN XY: 74250

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0238

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.219

Alfa AF: 0.242 Hom.: 794

Bravo AF: 0.241

Asia WGS AF: 0.117 AC: 405 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8087095; hg19: chr18-51297743;