rs2085796

Variant names:

• chr18-43805572-A-G
• rs2085796

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 0.462 in 152,010 control chromosomes in the GnomAD database, including 16,711 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 0.46 (16711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 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: 0.462 AC: 70223 AN: 151892 Hom.: 16700 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.462 AC: 70259 AN: 152010 Hom.: 16711 Cov.: 32 AF XY: 0.459 AC XY: 34078 AN XY: 74318

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.446

Alfa AF: 0.477 Hom.: 2978

Bravo AF: 0.449

Asia WGS AF: 0.283 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2085796; hg19: chr18-41385537;