rs4799386

Variant names:

• chr18-35507104-C-A
• rs4799386

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 0.372 in 151,986 control chromosomes in the GnomAD database, including 11,176 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 0.37 (11176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.476 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: 0.372 AC: 56559 AN: 151870 Hom.: 11166 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.372 AC: 56596 AN: 151986 Hom.: 11176 Cov.: 32 AF XY: 0.374 AC XY: 27800 AN XY: 74278

African (AFR) AF: 0.248 AC: 10253 AN: 41420

American (AMR) AF: 0.485 AC: 7417 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1434 AN: 3464

East Asian (EAS) AF: 0.452 AC: 2337 AN: 5168

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4822

European-Finnish (FIN) AF: 0.388 AC: 4084 AN: 10538

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.404 AC: 27461 AN: 67974

Other (OTH) AF: 0.375 AC: 792 AN: 2110

Alfa AF: 0.401 Hom.: 21570

Bravo AF: 0.369

Asia WGS AF: 0.472 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0060
DANN	Benign	0.30
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs4799386; hg19: chr18-33087068;