18-30069772-G-A

Variant names:

• chr18-30069772-G-A
• rs3848487

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 0.933 in 152,222 control chromosomes in the GnomAD database, including 66,583 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 0.93 (66583 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.309
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.933 AC: 141909 AN: 152104 Hom.: 66533 Cov.: 33

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.933 AC: 142017 AN: 152222 Hom.: 66583 Cov.: 33 AF XY: 0.930 AC XY: 69185 AN XY: 74404

African (AFR) AF: 0.887 AC: 36845 AN: 41532

American (AMR) AF: 0.877 AC: 13395 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.981 AC: 3401 AN: 3468

East Asian (EAS) AF: 0.726 AC: 3739 AN: 5152

South Asian (SAS) AF: 0.934 AC: 4507 AN: 4826

European-Finnish (FIN) AF: 0.967 AC: 10273 AN: 10622

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66697 AN: 68030

Other (OTH) AF: 0.945 AC: 1999 AN: 2116

Alfa AF: 0.965 Hom.: 33772

Bravo AF: 0.923

Asia WGS AF: 0.836 AC: 2897 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs3848487; hg19: chr18-27649737;