chr18-75090996-A-G

Position:

• chr18-75090996-A-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 0.882 in 152,290 control chromosomes in the GnomAD database, including 59,609 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 0.88 (59609 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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: 0.882 AC: 134203 AN: 152172 Hom.: 59563 Cov.: 34

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.882 AC: 134309 AN: 152290 Hom.: 59609 Cov.: 34 AF XY: 0.877 AC XY: 65303 AN XY: 74460

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.937

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.892

Alfa AF: 0.926 Hom.: 37459

Bravo AF: 0.882

Asia WGS AF: 0.805 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876486; hg19: chr18-72802952;