chr18-50954471-T-C

Position:

• chr18-50954471-T-C

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 0.688 in 151,898 control chromosomes in the GnomAD database, including 36,313 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 0.69 (36313 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.768 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: 0.688 AC: 104380 AN: 151780 Hom.: 36281 Cov.: 30

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.688 AC: 104468 AN: 151898 Hom.: 36313 Cov.: 30 AF XY: 0.688 AC XY: 51037 AN XY: 74218

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.699

Alfa AF: 0.665 Hom.: 7501

Bravo AF: 0.702

Asia WGS AF: 0.699 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs685373; hg19: chr18-48480841;