rs4798896

chr18-78152922-A-G

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 0.391 in 151,998 control chromosomes in the GnomAD database, including 12,142 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 0.39 (12142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59282 AN: 151878 Hom.: 12113 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.391 AC: 59361 AN: 151998 Hom.: 12142 Cov.: 32 AF XY: 0.389 AC XY: 28890 AN XY: 74292

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.344

Alfa AF: 0.350 Hom.: 9790

Bravo AF: 0.393

Asia WGS AF: 0.399 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.28
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4798896; hg19: chr18-75912922; COSMIC: COSV62903255;