rs4799585

Positions:

• chr18-31610211-C-T

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 0.271 in 152,042 control chromosomes in the GnomAD database, including 5,877 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 0.27 (5877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.307 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: 0.271 AC: 41226 AN: 151924 Hom.: 5876 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.271 AC: 41245 AN: 152042 Hom.: 5877 Cov.: 32 AF XY: 0.270 AC XY: 20034 AN XY: 74316

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.306

Alfa AF: 0.312 Hom.: 11105

Bravo AF: 0.270

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	7.9
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4799585; hg19: chr18-29190174;