18-77160709-C-T

Variant names:

• chr18-77160709-C-T
• rs1812680

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 0.665 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.665 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

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.652

Alfa AF: 0.666 Hom.: 15923

Bravo AF: 0.663

Asia WGS AF: 0.729 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1812680; hg19: chr18-74872665;