18-55195877-C-G

Position:

• chr18-55195877-C-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 0.268 in 149,262 control chromosomes in the GnomAD database, including 5,830 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 0.27 (5830 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55195877C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.268 AC: 39980 AN: 149214 Hom.: 5833 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.268 AC: 39992 AN: 149262 Hom.: 5830 Cov.: 31 AF XY: 0.272 AC XY: 19771 AN XY: 72580

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.283

Alfa AF: 0.283 Hom.: 3416

Bravo AF: 0.257

Asia WGS AF: 0.400 AC: 1389 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1970671; hg19: chr18-52863108;