chr18-77160709-C-T

Position:

• chr18-77160709-C-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.77160709C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;