18-69235980-G-C

Variant names:

• chr18-69235980-G-C
• rs661087

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.931

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.924

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs661087; hg19: chr18-66903217;