rs4798765

Variant names:

• chr18-9083405-T-C
• rs4798765

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 0.649 in 152,082 control chromosomes in the GnomAD database, including 32,217 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 0.65 (32217 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.732 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: 0.650 AC: 98707 AN: 151964 Hom.: 32205 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.649 AC: 98765 AN: 152082 Hom.: 32217 Cov.: 32 AF XY: 0.656 AC XY: 48753 AN XY: 74330

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.648

Alfa AF: 0.659 Hom.: 33326

Bravo AF: 0.637

Asia WGS AF: 0.666 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4798765; hg19: chr18-9083403;