18-60006567-A-G

Variant names:

• chr18-60006567-A-G
• rs12964056

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 0.594 in 151,864 control chromosomes in the GnomAD database, including 28,508 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 0.59 (28508 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 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: 0.594 AC: 90155 AN: 151746 Hom.: 28502 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.594 AC: 90173 AN: 151864 Hom.: 28508 Cov.: 31 AF XY: 0.591 AC XY: 43857 AN XY: 74198

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.671

Gnomad4 EAS AF: 0.669

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.621

Alfa AF: 0.645 Hom.: 3926

Bravo AF: 0.589

Asia WGS AF: 0.569 AC: 1982 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12964056; hg19: chr18-57673799;