18-60270226-A-G

Variant names:

• chr18-60270226-A-G
• rs718475

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 0.223 in 151,988 control chromosomes in the GnomAD database, including 4,644 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 0.22 (4644 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33950 AN: 151872 Hom.: 4642 Cov.: 32

Gnomad AFR AF: 0.0845

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.223 AC: 33946 AN: 151988 Hom.: 4644 Cov.: 32 AF XY: 0.219 AC XY: 16261 AN XY: 74300

Gnomad4 AFR AF: 0.0842

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.221

Alfa AF: 0.261 Hom.: 719

Bravo AF: 0.209

Asia WGS AF: 0.169 AC: 586 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718475; hg19: chr18-57937459;