chr18-77160709-C-T

Variant names:

• chr18-77160709-C-T
• rs1812680

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 0.665 in 152,102 control chromosomes in the GnomAD database, including 33,948 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 0.66 (33948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101026 AN: 151984 Hom.: 33925 Cov.: 33

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.665 AC: 101088 AN: 152102 Hom.: 33948 Cov.: 33 AF XY: 0.668 AC XY: 49717 AN XY: 74378

African (AFR) AF: 0.574 AC: 23786 AN: 41454

American (AMR) AF: 0.693 AC: 10585 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2343 AN: 3466

East Asian (EAS) AF: 0.871 AC: 4513 AN: 5182

South Asian (SAS) AF: 0.649 AC: 3133 AN: 4824

European-Finnish (FIN) AF: 0.759 AC: 8038 AN: 10588

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46525 AN: 67994

Other (OTH) AF: 0.652 AC: 1378 AN: 2114

Alfa AF: 0.666 Hom.: 17817

Bravo AF: 0.663

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.80
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1812680; hg19: chr18-74872665;