18-565414-A-G

Variant names:

• chr18-565414-A-G
• rs508969

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.788 AC: 32684 AN: 41484

American (AMR) AF: 0.857 AC: 13099 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2895 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5138 AN: 5160

South Asian (SAS) AF: 0.854 AC: 4115 AN: 4818

European-Finnish (FIN) AF: 0.757 AC: 8018 AN: 10586

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50663 AN: 67980

Other (OTH) AF: 0.799 AC: 1685 AN: 2110

Alfa AF: 0.771 Hom.: 6396

Bravo AF: 0.792

Asia WGS AF: 0.924 AC: 3214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs508969; hg19: chr18-565414;