chr18-6939948-G-A

Variant names:

• chr18-6939948-G-A
• rs597503

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 0.859 in 152,258 control chromosomes in the GnomAD database, including 56,312 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 0.86 (56312 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 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: 0.859 AC: 130674 AN: 152140 Hom.: 56283 Cov.: 33

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.859 AC: 130762 AN: 152258 Hom.: 56312 Cov.: 33 AF XY: 0.860 AC XY: 64024 AN XY: 74450

African (AFR) AF: 0.822 AC: 34124 AN: 41530

American (AMR) AF: 0.848 AC: 12979 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3090 AN: 3468

East Asian (EAS) AF: 0.836 AC: 4326 AN: 5176

South Asian (SAS) AF: 0.825 AC: 3982 AN: 4826

European-Finnish (FIN) AF: 0.949 AC: 10074 AN: 10614

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.875 AC: 59498 AN: 68024

Other (OTH) AF: 0.846 AC: 1789 AN: 2114

Alfa AF: 0.867 Hom.: 163691

Bravo AF: 0.851

Asia WGS AF: 0.837 AC: 2910 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs597503; hg19: chr18-6939947;