18-79779764-C-A

Position:

• chr18-79779764-C-A

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 0.464 in 152,132 control chromosomes in the GnomAD database, including 19,207 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 0.46 (19207 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70587 AN: 152014 Hom.: 19205 Cov.: 34

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.464 AC: 70604 AN: 152132 Hom.: 19207 Cov.: 34 AF XY: 0.465 AC XY: 34607 AN XY: 74346

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.502

Alfa AF: 0.564 Hom.: 32754

Bravo AF: 0.437

Asia WGS AF: 0.574 AC: 1997 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	0.36
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs585811; hg19: chr18-77539764;