chr18-43805572-A-G

Variant names:

• chr18-43805572-A-G
• rs2085796

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 0.462 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.450 AC: 18649 AN: 41440

American (AMR) AF: 0.381 AC: 5804 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1911 AN: 3472

East Asian (EAS) AF: 0.111 AC: 576 AN: 5174

South Asian (SAS) AF: 0.425 AC: 2049 AN: 4824

European-Finnish (FIN) AF: 0.523 AC: 5523 AN: 10562

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34300 AN: 67970

Other (OTH) AF: 0.446 AC: 942 AN: 2112

Alfa AF: 0.476 Hom.: 3057

Bravo AF: 0.449

Asia WGS AF: 0.283 AC: 991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.33
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2085796; hg19: chr18-41385537;