18-565414-A-G

Variant names:

• chr18-565414-A-G
• rs508969

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 0.784 in 152,100 control chromosomes in the GnomAD database, including 46,969 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 0.78 (46969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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: 0.784 AC: 119114 AN: 151982 Hom.: 46926 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.784 AC: 119216 AN: 152100 Hom.: 46969 Cov.: 32 AF XY: 0.789 AC XY: 58680 AN XY: 74346

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.854

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.799

Alfa AF: 0.771 Hom.: 6160

Bravo AF: 0.792

Asia WGS AF: 0.924 AC: 3214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs508969; hg19: chr18-565414;