rs2085796

chr18-43805572-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 0.462 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;