chr18-69269511-G-C

Variant names:

• chr18-69269511-G-C
• rs509030

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 0.37 in 151,950 control chromosomes in the GnomAD database, including 11,447 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 0.37 (11447 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.10
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56255 AN: 151830 Hom.: 11439 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.370 AC: 56280 AN: 151950 Hom.: 11447 Cov.: 33 AF XY: 0.370 AC XY: 27434 AN XY: 74228

African (AFR) AF: 0.197 AC: 8191 AN: 41480

American (AMR) AF: 0.480 AC: 7316 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1499 AN: 3464

East Asian (EAS) AF: 0.452 AC: 2333 AN: 5156

South Asian (SAS) AF: 0.504 AC: 2428 AN: 4816

European-Finnish (FIN) AF: 0.345 AC: 3640 AN: 10546

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29619 AN: 67918

Other (OTH) AF: 0.390 AC: 822 AN: 2110

Alfa AF: 0.383 Hom.: 1477

Bravo AF: 0.372

Asia WGS AF: 0.459 AC: 1590 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.64
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs509030; hg19: chr18-66936747;