chr18-60210922-G-A

Position:

• chr18-60210922-G-A

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 0.0925 in 151,986 control chromosomes in the GnomAD database, including 782 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 0.092 (782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 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: 0.0925 AC: 14045 AN: 151866 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.00675

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.0925 AC: 14057 AN: 151986 Hom.: 782 Cov.: 32 AF XY: 0.0955 AC XY: 7093 AN XY: 74278

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0506

Gnomad4 ASJ AF: 0.0649

Gnomad4 EAS AF: 0.00657

Gnomad4 SAS AF: 0.0953

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0721

Gnomad4 OTH AF: 0.0747

Alfa AF: 0.0716 Hom.: 589

Bravo AF: 0.0854

Asia WGS AF: 0.0600 AC: 206 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8094523; hg19: chr18-57878155;