rs4798896

Variant names:

• chr18-78152922-A-G
• rs4798896

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.490 AC: 20294 AN: 41438

American (AMR) AF: 0.361 AC: 5518 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3472

East Asian (EAS) AF: 0.366 AC: 1884 AN: 5154

South Asian (SAS) AF: 0.381 AC: 1830 AN: 4804

European-Finnish (FIN) AF: 0.364 AC: 3852 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24097 AN: 67962

Other (OTH) AF: 0.344 AC: 727 AN: 2116

Alfa AF: 0.365 Hom.: 27630

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

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