rs1587893

Variant names:

• chr18-78178925-T-C
• rs1587893

Your query was ambiguous. Multiple possible variants found:

• chr18-78178925-T-C
• chr18-78178925-T-G

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 0.75 in 152,172 control chromosomes in the GnomAD database, including 43,791 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 0.75 (43791 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 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: 0.750 AC: 114053 AN: 152054 Hom.: 43740 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.750 AC: 114159 AN: 152172 Hom.: 43791 Cov.: 33 AF XY: 0.745 AC XY: 55446 AN XY: 74386

African (AFR) AF: 0.913 AC: 37939 AN: 41550

American (AMR) AF: 0.704 AC: 10760 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.759 AC: 2631 AN: 3468

East Asian (EAS) AF: 0.489 AC: 2524 AN: 5160

South Asian (SAS) AF: 0.742 AC: 3580 AN: 4822

European-Finnish (FIN) AF: 0.637 AC: 6730 AN: 10566

Middle Eastern (MID) AF: 0.750 AC: 219 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47527 AN: 67998

Other (OTH) AF: 0.737 AC: 1559 AN: 2114

Alfa AF: 0.720 Hom.: 15405

Bravo AF: 0.758

Asia WGS AF: 0.660 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1587893; hg19: chr18-75938925;