chr18-44182626-C-T

Position:

• chr18-44182626-C-T

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 0.0165 in 152,140 control chromosomes in the GnomAD database, including 125 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 0.016 (125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0164 AC: 2495 AN: 152022 Hom.: 121 Cov.: 32

Gnomad AFR AF: 0.00246

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00474

Gnomad OTH AF: 0.0173

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

GnomAD4 genome AF: 0.0165 AC: 2508 AN: 152140 Hom.: 125 Cov.: 32 AF XY: 0.0181 AC XY: 1344 AN XY: 74376

Gnomad4 AFR AF: 0.00246

Gnomad4 AMR AF: 0.0866

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.00187

Gnomad4 FIN AF: 0.00283

Gnomad4 NFE AF: 0.00474

Gnomad4 OTH AF: 0.0171

Alfa AF: 0.0176 Hom.: 34

Bravo AF: 0.0261

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.19
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502824; hg19: chr18-41762591;