rs1885592

Variant names:

• chr14-23668806-A-G
• rs1885592

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 0.477 in 152,030 control chromosomes in the GnomAD database, including 18,278 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 0.48 (18278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72555 AN: 151912 Hom.: 18278 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.477 AC: 72579 AN: 152030 Hom.: 18278 Cov.: 32 AF XY: 0.479 AC XY: 35564 AN XY: 74296

African (AFR) AF: 0.323 AC: 13409 AN: 41492

American (AMR) AF: 0.460 AC: 7030 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2137 AN: 3468

East Asian (EAS) AF: 0.353 AC: 1823 AN: 5168

South Asian (SAS) AF: 0.488 AC: 2344 AN: 4808

European-Finnish (FIN) AF: 0.591 AC: 6249 AN: 10566

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37678 AN: 67946

Other (OTH) AF: 0.516 AC: 1087 AN: 2106

Alfa AF: 0.526 Hom.: 88914

Bravo AF: 0.461

Asia WGS AF: 0.391 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.70
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1885592; hg19: chr14-24138015;