18-69235980-G-C

Variant names:

• chr18-69235980-G-C
• rs661087

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 0.919 in 152,214 control chromosomes in the GnomAD database, including 64,705 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 0.92 (64705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.968 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: 0.919 AC: 139711 AN: 152096 Hom.: 64652 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.919 AC: 139823 AN: 152214 Hom.: 64705 Cov.: 32 AF XY: 0.919 AC XY: 68409 AN XY: 74410

African (AFR) AF: 0.787 AC: 32644 AN: 41502

American (AMR) AF: 0.956 AC: 14610 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3383 AN: 3472

East Asian (EAS) AF: 0.970 AC: 5010 AN: 5164

South Asian (SAS) AF: 0.931 AC: 4501 AN: 4832

European-Finnish (FIN) AF: 0.966 AC: 10260 AN: 10618

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66269 AN: 68032

Other (OTH) AF: 0.924 AC: 1951 AN: 2112

Alfa AF: 0.943 Hom.: 7949

Bravo AF: 0.913

Asia WGS AF: 0.931 AC: 3239 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	3.2
DANN	Benign	0.62
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs661087; hg19: chr18-66903217;