rs9675979

Variant names:

• chr18-67964346-A-G
• rs9675979

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 0.855 in 151,870 control chromosomes in the GnomAD database, including 55,629 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 0.85 (55629 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.855 AC: 129730 AN: 151752 Hom.: 55581 Cov.: 29

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.895

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.855 AC: 129833 AN: 151870 Hom.: 55629 Cov.: 29 AF XY: 0.856 AC XY: 63517 AN XY: 74196

African (AFR) AF: 0.820 AC: 33956 AN: 41388

American (AMR) AF: 0.896 AC: 13671 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2942 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5046 AN: 5070

South Asian (SAS) AF: 0.807 AC: 3882 AN: 4812

European-Finnish (FIN) AF: 0.886 AC: 9367 AN: 10572

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58090 AN: 67982

Other (OTH) AF: 0.875 AC: 1840 AN: 2104

Alfa AF: 0.854 Hom.: 78322

Bravo AF: 0.858

Asia WGS AF: 0.902 AC: 3135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs9675979; hg19: chr18-65631583;