18-61155377-T-G

Position:

• chr18-61155377-T-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 0.0384 in 152,292 control chromosomes in the GnomAD database, including 166 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 0.038 (166 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0724 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: 0.0382 AC: 5819 AN: 152174 Hom.: 165 Cov.: 33

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.0287

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0384 AC: 5843 AN: 152292 Hom.: 166 Cov.: 33 AF XY: 0.0392 AC XY: 2918 AN XY: 74470

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.0330

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.0471

Gnomad4 SAS AF: 0.0639

Gnomad4 FIN AF: 0.0287

Gnomad4 NFE AF: 0.0173

Gnomad4 OTH AF: 0.0360

Alfa AF: 0.00880 Hom.: 2

Bravo AF: 0.0401

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9319974; hg19: chr18-58822610;